instance_id stringlengths 10 57 | file_changes listlengths 1 15 | repo stringlengths 7 53 | base_commit stringlengths 40 40 | problem_statement stringlengths 11 52.5k | patch stringlengths 251 7.06M |
|---|---|---|---|---|---|
nilearn__nilearn-4503 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/04_glm_first_level/plot_design_matrix.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities... | nilearn/nilearn | 796f101439c6ff72434a7adb3ab1fecf2cf87e21 | :rotating_light: NIGHTLY DEPENDENCIES TEST: failure on `refs/heads/main`
The run `10297598102` of the workflow testing Nilearn with the nightly build of its dependencies failed on `refs/heads/main`.
You can view the report here: https://github.com/nilearn/nilearn/actions/runs/10297598102
Pinging @nilearn/core
| diff --git a/.github/workflows/nightly_dependencies.yml b/.github/workflows/nightly_dependencies.yml
index 621ba7d31..a7c4c3f21 100644
--- a/.github/workflows/nightly_dependencies.yml
+++ b/.github/workflows/nightly_dependencies.yml
@@ -19,6 +19,10 @@ on:
workflow_dispatch:
+# Force to use color
+env:
+ FOR... |
nilearn__nilearn-4507 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/_utils/data_gen.py:_write_fake_bold_gifti",
"nilearn/_utils/data_gen.py:create_fake_bids_dataset",
"nilearn/_utils/data_gen.py:_mock_bids_derivatives",
"nilearn/_utils/da... | nilearn/nilearn | aca81412fceeee04cf9ecc9ea46e69c72880f21b | Adapt first_level_from_bids to run on surface images directly | diff --git a/nilearn/_utils/data_gen.py b/nilearn/_utils/data_gen.py
index cc5ee76e4..def082c86 100644
--- a/nilearn/_utils/data_gen.py
+++ b/nilearn/_utils/data_gen.py
@@ -11,7 +11,7 @@ import numpy as np
import pandas as pd
import scipy.linalg
import scipy.signal
-from nibabel import Nifti1Image
+from nibabel impo... |
nilearn__nilearn-4558 | [
{
"changes": {
"added_entities": [
"nilearn/_utils/exceptions.py:AllVolumesRemovedError.__init__",
"nilearn/_utils/exceptions.py:AllVolumesRemovedError.__str__"
],
"added_modules": [
"nilearn/_utils/exceptions.py:AllVolumesRemovedError"
],
"edited_entities":... | nilearn/nilearn | 263ec16553757ef1ba18f76b003b16af264e9fbd | [BUG] `load_confounds` returns all nans when `sample_mask` is empty & `demean = True`
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Operating system
- [ ] Linux
- [X] Mac
- [ ] Windows
### Operating system version
MacOS Sequoia 15.0
### Python version
- ... | diff --git a/CITATION.cff b/CITATION.cff
index 733a4382f..17077d1fd 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -714,6 +714,10 @@ authors:
- given-names: Vasco
family-names: Diogo
website: https://github.com/vascosa
+ - given-names: Victoria
+ family-names: Shevchenko
+ website: https://github.c... |
nilearn__nilearn-4582 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
... | nilearn/nilearn | dcd92aa357ab3a751161aeea2edfa3a775ae644f | `first_level_from_bids` should return subjects in order
If subjects labels are passe, then `first_level_from_bids` will loop over subjects in a random order (uses `set` to avoid duplicates):
https://github.com/nilearn/nilearn/blob/51778dd58d78036afdef7b47ae3137ff0dbda290/nilearn/glm/first_level/first_level.py#L1684... | diff --git a/CITATION.cff b/CITATION.cff
index 3a6cb448b..e332aa8df 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -755,3 +755,6 @@ authors:
family-names: Nájera
website: https://github.com/Titan-C
affiliation: Checkmk
+ - given-names: Tharun
+ family-names: K
+ website: https://github.com/tharun... |
nilearn__nilearn-4631 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "maint_tools/check_gha_workflow.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ni... | nilearn/nilearn | 524ee463e85c787a0d605afd635bc47158abcf46 | Replace the use of `tempfile` in tests with proper pytest fixtures.
Note to myself (not for this PR): the use of `tempfile` could be refactored with the proper pytest fixtures.
Would also avoid the manual removing of files for teardown.
_Originally posted by @Remi-Gau in https://github.com/nilearn/n... | diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml
index 1e8414c60..efc5c5f2b 100644
--- a/.github/ISSUE_TEMPLATE/bug.yml
+++ b/.github/ISSUE_TEMPLATE/bug.yml
@@ -50,6 +50,7 @@ body:
label: Python version
description: What python version are you using?
options:
+ ... |
nilearn__nilearn-4636 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/interfaces/fmriprep/load_confounds.py:_check_strategy",
"nilearn/interfaces/fmriprep/load_confounds.py:load_confounds"
],
"edited_modules": [
"nilearn/interfaces/fmri... | nilearn/nilearn | 1634615fd113739fd5973de8cd093dd1503c2658 | [BUG] When using NiftiLabelsMasker with an empty confounds DataFrame, the masker raises an error
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Operating system
- [X] Linux
- [ ] Mac
- [ ] Windows
### Operating system version
- Linux Pop!_OS 22.04 LTS
### Python version... | diff --git a/CITATION.cff b/CITATION.cff
index 27e05206b..0516814af 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -772,3 +772,8 @@ authors:
family-names: Nájera
website: https://github.com/Titan-C
affiliation: Checkmk
+ - given-names: Micha
+ family-names: Burkhardt
+ website: https://github.com... |
nilearn__nilearn-4701 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/datasets/_utils.py:fetch_single_file"
],
"edited_modules": [
"nilearn/datasets/_utils.py:fetch_single_file"
]
},
"file": "nilearn/datasets/_utils.py"
}
] | nilearn/nilearn | 567498d5a6d7766ebebbb6aa2c186786a5ea3534 | local_file never set to an actual value
I think this is a bug. These lines do not seem to be covered by the current tests, and `local_file` is set to `None` at Line ~574 and never changed after, so as far as I can tell the file opening should fail regardless of which function/method is used. I guess it is... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6dbefaaec..1d39726c1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -74,7 +74,7 @@ repos:
)$
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.6.9
+ rev: v0.7.2
hooks:
# Run the lin... |
nilearn__nilearn-4715 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/04_glm_first_level/plot_localizer_surface_analysis.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"ed... | nilearn/nilearn | a88a118ef93349853cae2d531d7b2600d5b5868a | support 2nd level GLM analysis of SurfaceImage objects
Realizing that we do not support 2nd level analysis of SurfaceImage objects?
@bthirion This is something we want to have, right?
_Originally posted by @Remi-Gau in https://github.com/nilearn/nilearn/issues/4603#issuecomment-2397105199_
... | diff --git a/examples/04_glm_first_level/plot_localizer_surface_analysis.py b/examples/04_glm_first_level/plot_localizer_surface_analysis.py
index c2fdd593f..08269684a 100644
--- a/examples/04_glm_first_level/plot_localizer_surface_analysis.py
+++ b/examples/04_glm_first_level/plot_localizer_surface_analysis.py
@@ -96,... |
nilearn__nilearn-4770 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/datasets/atlas.py:_compute_symmetric_split"
],
"edited_modules": [
"nilearn/datasets/atlas.py:_compute_symmetric_split"
]
},
"file": "nilearn/datasets/atlas.py"... | nilearn/nilearn | 4aadde46366d610b5d13699b8f7716d8c09e7159 | run fit and transform of SurfaceLabelsMasker on list of Surface image
After that I think I will do something similar for the label masker.
_Originally posted by @Remi-Gau in https://github.com/nilearn/nilearn/issues/4719#issuecomment-2483234819_
| diff --git a/nilearn/datasets/atlas.py b/nilearn/datasets/atlas.py
index 89125e3c0..57924787f 100644
--- a/nilearn/datasets/atlas.py
+++ b/nilearn/datasets/atlas.py
@@ -804,10 +804,10 @@ def _compute_symmetric_split(source, atlas_niimg, names):
if source == "Juelich":
for idx, name in enumerate(names):
... |
nilearn__nilearn-4795 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"maint_tools/check_gha_workflow.py:_update_jobs_data"
],
"edited_modules": [
"maint_tools/check_gha_workflow.py:_update_jobs_data"
]
},
"file": "maint_tools/check_gha_wo... | nilearn/nilearn | aca81412fceeee04cf9ecc9ea46e69c72880f21b | [DOC] inconsistent Doc style for classes
### Is there an existing issue for this?
- [x] I have searched the existing issues
### Describe your proposed suggestion in detail.
Classes where parameters for instanciation are documented after the constructor.
For example Contrasts
https://nilearn.github.io/dev/modules/... | diff --git a/README.rst b/README.rst
index d1df8aec5..6be9b0acc 100644
--- a/README.rst
+++ b/README.rst
@@ -10,7 +10,7 @@
:target: https://github.com/nilearn/nilearn/actions
:alt: Github Actions Build Status
-.. image:: https://codecov.io/gh/nilearn/nilearn/branch/main/graph/badge.svg
+.. image:: https://c... |
nilearn__nilearn-4796 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"maint_tools/check_gha_workflow.py:_update_jobs_data"
],
"edited_modules": [
"maint_tools/check_gha_workflow.py:_update_jobs_data"
]
},
"file": "maint_tools/check_gha_wo... | nilearn/nilearn | aca81412fceeee04cf9ecc9ea46e69c72880f21b | :rotating_light: NIGHTLY DEPENDENCIES TEST: failure on `refs/heads/main`
The run `12046699245` of the workflow testing Nilearn with the nightly build of its dependencies failed on `refs/heads/main`.
You can view the report here: https://github.com/nilearn/nilearn/actions/runs/12046699245
Pinging @nilearn/core
| diff --git a/README.rst b/README.rst
index d1df8aec5..6be9b0acc 100644
--- a/README.rst
+++ b/README.rst
@@ -10,7 +10,7 @@
:target: https://github.com/nilearn/nilearn/actions
:alt: Github Actions Build Status
-.. image:: https://codecov.io/gh/nilearn/nilearn/branch/main/graph/badge.svg
+.. image:: https://c... |
nilearn__nilearn-4802 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/07_advanced/plot_beta_series.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | nilearn/nilearn | b734e7af7f886de41daf19f3d030d89ac6f2c2c7 | Localizer BIDS dataset derivative not BIDS compliant
This caused some examples to fail because our the BIDS derivatives files in our example dataset are not proper derivatives: they do not have a space entity.
- examples/07_advanced/plot_beta_series.py
- examples/07_advanced/plot_bids_analysis.py
s... | diff --git a/examples/07_advanced/plot_beta_series.py b/examples/07_advanced/plot_beta_series.py
index 00e89bdf8..2adb3e58b 100644
--- a/examples/07_advanced/plot_beta_series.py
+++ b/examples/07_advanced/plot_beta_series.py
@@ -60,9 +60,6 @@ to build the LSS beta series.
"""
# sphinx_gallery_thumbnail_number = -2
... |
nilearn__nilearn-4804 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/signal.py:_check... | nilearn/nilearn | bd706ef5aff0426adf94c1b78f6ec5a3d5b62d3b | Checks on t_r type too stringent in signals
> **HOWEVER**
>
> There seems to be a minor bug:
>
> ```python
> from nilearn.maskers import NiftiMasker
> from nilearn import datasets
>
> dataset = datasets.fetch_development_fmri(n_subjects=10)
>
> func_filename = dataset.func[0]
>
> masker = NiftiMasker(
> detren... | diff --git a/doc/conf.py b/doc/conf.py
index 5eb72f5ec..ffec65803 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -171,13 +171,10 @@ suppress_warnings = ["image.not_readable", "config.cache"]
html_theme = "furo"
# Add custom css instructions from themes/custom.css
-font_awesome = "https://cdnjs.cloudflare.com/ajax/li... |
nilearn__nilearn-4806 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "nilearn/_utils/docs.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/glm/s... | nilearn/nilearn | 8318065a433186d0553db281fcf634f21c46ca48 | Passing a 4D image to `SecondLevelModel`
<!--Provide a brief description of the bug.-->
See this [Neurostars post](https://neurostars.org/t/nilearn-second-level-error-img-slicer/20659)
When passing a 4D image to `SecondLevelModel.fit()`, no error is raise although the documentation says that possible input values ... | diff --git a/nilearn/_utils/docs.py b/nilearn/_utils/docs.py
index 170347fcc..65246f1b7 100644
--- a/nilearn/_utils/docs.py
+++ b/nilearn/_utils/docs.py
@@ -750,7 +750,8 @@ docdict["second_level_input"] = """
second_level_input : :obj:`list` of \
:class:`~nilearn.glm.first_level.FirstLevelModel` objects or \
... |
nilearn__nilearn-4809 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "nilearn/_utils/docs.py"
},
{
"changes": {
"added_entities": [
"nilearn/_utils/param_validation.py:check_reduction_strategy"
],
... | nilearn/nilearn | 9c22285597dcaf95018a224318bcf3b0bdaca3ad | [ENH] implement strategies in SurfaceLabelMasker
nilearn.maskers.NiftiLabelsMasker and nilearn.regions.img_to_signals_labels have a way to summarize data from a region using different strategies: sum, mean, median, minimum, maximum, variance, standard_deviation.
![Image](https://github.com/user-attachments/assets/52f3... | diff --git a/nilearn/_utils/docs.py b/nilearn/_utils/docs.py
index c046f616a..7fb68c1c5 100644
--- a/nilearn/_utils/docs.py
+++ b/nilearn/_utils/docs.py
@@ -939,6 +939,14 @@ standardize_confounds : :obj:`bool`, default=True
their mean is put to 0 and their variance to 1 in the time dimension.
"""
+# standardize... |
nilearn__nilearn-4857 | [
{
"changes": {
"added_entities": [
"nilearn/mass_univariate/permuted_least_squares.py:_make_array_contiguous",
"nilearn/mass_univariate/permuted_least_squares.py:_compute_t_stat_threshold"
],
"added_modules": [
"nilearn/mass_univariate/permuted_least_squares.py:_make_ar... | nilearn/nilearn | b7c94a0ddbf823c54385dcdbd5ecff0431a55509 | [BUG] Some new test failures on s390x (big-endian) in 0.11.0
### Is there an existing issue for this?
- [x] I have searched the existing issues
### Operating system
- [x] Linux
- [ ] Mac
- [ ] Windows
### Operating system version
Fedora Rawhide, or 41
### Python version
- [x] 3.13
- [ ] 3.12
- [ ] 3.11
- [ ] 3.1... | diff --git a/nilearn/mass_univariate/permuted_least_squares.py b/nilearn/mass_univariate/permuted_least_squares.py
index 1133a0e75..d66c3bbfe 100644
--- a/nilearn/mass_univariate/permuted_least_squares.py
+++ b/nilearn/mass_univariate/permuted_least_squares.py
@@ -193,7 +193,6 @@ def _permuted_ols_on_chunk(
... |
nilearn__nilearn-4903 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/_utils/data_gen.... | nilearn/nilearn | c4258e942754e6630ad89891214cc9903e3e203b | :rotating_light: NIGHTLY DEPENDENCIES TEST: failure on `refs/heads/main`
The run `12199328751` of the workflow testing Nilearn with the nightly build of its dependencies failed on `refs/heads/main`.
You can view the report here: https://github.com/nilearn/nilearn/actions/runs/12199328751
Pinging @nilearn/core
| diff --git a/doc/conf.py b/doc/conf.py
index 736060512..1e4463b61 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -183,6 +183,7 @@ linkcheck_ignore = [
"https://pages.saclay.inria.fr/bertrand.thirion/",
"https://pages.stern.nyu.edu/~wgreene/Text/econometricanalysis.htm",
"http://brainomics.cea.fr/localizer... |
nilearn__nilearn-4929 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/datasets/atlas.py:fetch_atlas_pauli_2017"
],
"edited_modules": [
"nilearn/datasets/atlas.py:fetch_atlas_pauli_2017"
]
},
"file": "nilearn/datasets/atlas.py"
}... | nilearn/nilearn | cd17602ed281f5ebfb8b29f7178539344682acfd | Improper parameter name & non-optimal args for atlas Pauli 2017
The `version` parameter for :func:`nilearn.datasets.fetch_atlas_pauli_2017` is a weird name. Version makes me think of numbers and iterations, and chronological versions of atlases, not the type of atlas. We should change it to `type`.
Additionally, cur... | diff --git a/nilearn/datasets/atlas.py b/nilearn/datasets/atlas.py
index cac8de1c0..bce0bfb04 100644
--- a/nilearn/datasets/atlas.py
+++ b/nilearn/datasets/atlas.py
@@ -13,14 +13,14 @@ import pandas as pd
from nibabel import freesurfer, load
from sklearn.utils import Bunch
-from .._utils import check_niimg, fill_do... |
nilearn__nilearn-4939 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/regions/hierarchical_kmeans_clustering.py:HierarchicalKMeans.fit",
"nilearn/regions/hierarchical_kmeans_clustering.py:HierarchicalKMeans.transform",
"nilearn/regions/hierarchical... | nilearn/nilearn | d57c0d86e991e8de5fed4ab1ff9fc8350ddeeb90 | [BUG] `HierarchicalKMeans.fit()` takes transposed X
.... I noticed that `HierarchicalKMeans.fit()` takes transposed X:
https://github.com/nilearn/nilearn/blob/135e5388386c24ca879328040273127f8acb4a6a/nilearn/regions/hierarchical_kmeans_clustering.py#L233
See in `ReNA.fit()` for comparison:
https://github.com/nilea... | diff --git a/nilearn/regions/hierarchical_kmeans_clustering.py b/nilearn/regions/hierarchical_kmeans_clustering.py
index 3949170f4..457f1b113 100644
--- a/nilearn/regions/hierarchical_kmeans_clustering.py
+++ b/nilearn/regions/hierarchical_kmeans_clustering.py
@@ -259,7 +259,7 @@ class HierarchicalKMeans(ClusterMixin, ... |
nilearn__nilearn-4967 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nilearn/_utils/glm.py:check_and_load_tables"
],
"edited_modules": [
"nilearn/_utils/glm.py:check_and_load_tables"
]
},
"file": "nilearn/_utils/glm.py"
},
{
"cha... | nilearn/nilearn | d57c0d86e991e8de5fed4ab1ff9fc8350ddeeb90 | GLM confounds as numpy array are not supported
ok something does not make sense about allowing numpy array: they are accepted as inputs but never appended to the output list... so they will never be passed on to whatever needs them later...
I think that in a follow up PR I will check if we actually support array as ... | diff --git a/nilearn/_utils/glm.py b/nilearn/_utils/glm.py
index 5e61fb3f8..4c1233373 100644
--- a/nilearn/_utils/glm.py
+++ b/nilearn/_utils/glm.py
@@ -13,6 +13,8 @@ def check_and_load_tables(tables_to_check, var_name):
if they are pandas.DataFrame, \
or a CSV or TSV file that can be loaded to a pandas... |
nilearn__nilearn-4991 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/01_plotting/plot_3d_map_to_surface_projection.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_... | nilearn/nilearn | cd2871895581caacfcbd2bb443fa5d54304d94b5 | [ENH] nilearn.plotting.view_surf for both hemispheres?
### Is there an existing issue for this?
- [x] I have searched the existing issues
### Describe your proposed enhancement in detail.
Is there a plan to enhance `nilearn.plotting.view_surf` to show both hemispheres simultaneously?
### Benefits to the change
Ins... | diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 7b2866482..f6584384b 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -99,7 +99,7 @@ jobs:
echo "BUILD = $(cat build.txt)"
echo "build=$(cat build.txt)" >> $GIT... |
nilearn__nilearn-5017 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/02_decoding/plot_haxby_full_analysis.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities"... | nilearn/nilearn | 9761b402127b0186b8aa88a3977aefda4ebb5804 | modified example are not generated in PR
- seems recent: probably due to this https://github.com/nilearn/nilearn/pull/4984 | diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 17089d5a1..3e1fd52f1 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -85,7 +85,9 @@ jobs:
- name: Checkout nilearn
uses: actions/checkout@v4
with:
+ ... |
nilearn__nilearn-5059 | [
{
"changes": {
"added_entities": [
"nilearn/_utils/class_inspect.py:is_multimasker",
"nilearn/_utils/class_inspect.py:check_masker_clean_kwargs",
"nilearn/_utils/class_inspect.py:check_nifti_masker_detrending",
"nilearn/_utils/class_inspect.py:check_surface_masker_detrendin... | nilearn/nilearn | b851ecc5a14a6d11aa9f8c2aa59cbede493e699f | [ENH] Add Tests to Better Cover the Cleaning Behavior of Maskers
Description:
Following discussions in [PR #3437](https://github.com/nilearn/nilearn/pull/3437), it was identified that the cleaning functionality in maskers is not sufficiently covered by tests. Specifically:
The cleaning functionality relies heavily on... | diff --git a/nilearn/_utils/class_inspect.py b/nilearn/_utils/class_inspect.py
index 730bcfd61..d5903c611 100644
--- a/nilearn/_utils/class_inspect.py
+++ b/nilearn/_utils/class_inspect.py
@@ -2,6 +2,7 @@
import numpy as np
from nibabel import Nifti1Image
+from numpy.testing import assert_array_equal, assert_raises... |
nilearn__nilearn-5097 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/01_plotting/plot_carpet.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | nilearn/nilearn | d979bacad0dfd0600e35a23f9f08d3df7907e489 | [BUG] `plot_haxby_understand_decoder.py` does not show that nilearn and sklearn coincincde when using penalty='l1'
### Is there an existing issue for this?
- [x] I have searched the existing issues
### Operating system
- [x] Linux
- [ ] Mac
- [ ] Windows
### Operating system version
For example one of the followi... | diff --git a/examples/01_plotting/plot_carpet.py b/examples/01_plotting/plot_carpet.py
index 8f6e60add..d393248a2 100644
--- a/examples/01_plotting/plot_carpet.py
+++ b/examples/01_plotting/plot_carpet.py
@@ -12,10 +12,10 @@ from a 4D functional image.
# %%
# Fetching data from ADHD dataset
# -----------------------... |
nilearn__nilearn-5142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/04_glm_first_level/plot_two_runs_model.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entitie... | nilearn/nilearn | 2a957f9c6b556716ca08b3c2f6c5fd2e0cabd0d3 | Add names for FIAC design matrices
Current report has no sense.
The best way is to embed the provided design matrices into a dataframe with proper column names. | diff --git a/examples/04_glm_first_level/plot_two_runs_model.py b/examples/04_glm_first_level/plot_two_runs_model.py
index 46ee677aa..9047ea246 100644
--- a/examples/04_glm_first_level/plot_two_runs_model.py
+++ b/examples/04_glm_first_level/plot_two_runs_model.py
@@ -6,9 +6,6 @@ Here, we will go through a full step-by... |
nilearn__nilearn-5169 | [
{
"changes": {
"added_entities": [
"nilearn/surface/surface.py:_mask_sample_locations",
"nilearn/surface/surface.py:_nearest_most_frequent"
],
"added_modules": [
"nilearn/surface/surface.py:_mask_sample_locations",
"nilearn/surface/surface.py:_nearest_most_frequ... | nilearn/nilearn | fefa4d30c262384ebda0f1123a1691abf466a9f0 | [BUG] _nearest_voxel_sampling does not truly perform nearest voxel interpolation
### Is there an existing issue for this?
- [x] I have searched the existing issues
### Operating system
- [x] Linux
- [ ] Mac
- [ ] Windows
### Operating system version
- Linux Ubuntu 22.04
### Python version
- [ ] 3.13
- [ ] 3.12
... | diff --git a/nilearn/surface/surface.py b/nilearn/surface/surface.py
index 4fbbfae4a..9d9686354 100644
--- a/nilearn/surface/surface.py
+++ b/nilearn/surface/surface.py
@@ -460,6 +460,60 @@ def _projection_matrix(
return proj
+def _mask_sample_locations(sample_locations, img_shape, mesh_n_vertices, mask):
+ ... |
nilearn__nilearn-5241 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/02_decoding/plot_haxby_searchlight.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": ... | nilearn/nilearn | defce5dc78faa2a4f1ad320307f2f02c43a9a127 | rename private function `_get_voxelwise_model_attribute`
as it now also handles vertices | diff --git a/examples/02_decoding/plot_haxby_searchlight.py b/examples/02_decoding/plot_haxby_searchlight.py
index 7486a3b86..914c4c48f 100644
--- a/examples/02_decoding/plot_haxby_searchlight.py
+++ b/examples/02_decoding/plot_haxby_searchlight.py
@@ -16,11 +16,11 @@ the :term:`fMRI` (see the generated figures).
# --... |
nilearn__nilearn-5242 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/02_decoding/plot_haxby_searchlight.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": ... | nilearn/nilearn | defce5dc78faa2a4f1ad320307f2f02c43a9a127 | Excessive number of warning when running searchlight
Just ran `examples/02_decoding/plot_haxby_searchlight.py` and getting MANY non convergence warning:
```
warnings.warn(
/home/remi/miniconda3/lib/python3.12/site-packages/sklearn/svm/_base.py:1235: ConvergenceWarning: Liblinear failed to converge, increase the numb... | diff --git a/examples/02_decoding/plot_haxby_searchlight.py b/examples/02_decoding/plot_haxby_searchlight.py
index 7486a3b86..914c4c48f 100644
--- a/examples/02_decoding/plot_haxby_searchlight.py
+++ b/examples/02_decoding/plot_haxby_searchlight.py
@@ -16,11 +16,11 @@ the :term:`fMRI` (see the generated figures).
# --... |
nilearn__nilearn-5263 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/06_manipulating_images/plot_extract_rois_statistical_maps.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
... | nilearn/nilearn | 3e073997c8008dccc2003ae049429a4e0272f432 | See if `check_embedded_masker` can be used more systematically across estimators
check_embedded_masker runs some checks on the masker of an estimator but only for those found in the decoding / decomposition subpackages.
https://github.com/nilearn/nilearn/blob/f5114ee0b831530907e554a669427e70837029d2/nilearn/_utils/mas... | diff --git a/examples/06_manipulating_images/plot_extract_rois_statistical_maps.py b/examples/06_manipulating_images/plot_extract_rois_statistical_maps.py
index 1278aa0cd..e82687271 100644
--- a/examples/06_manipulating_images/plot_extract_rois_statistical_maps.py
+++ b/examples/06_manipulating_images/plot_extract_rois... |
nion-software__niondata-20 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nion/data/Core.py:function_register_template"
],
"edited_modules": [
"nion/data/Core.py:function_register_template"
]
},
"file": "nion/data/Core.py"
}
] | nion-software/niondata | 422c897b7a2295ad907b7beaef73dcae5a2ca520 | Should register_template return offset relative to center pixel?
```
quality, offset = xd.register_template(img, tmpl_img)
offset = Geometry.FloatPoint(y=img.data_shape[0] * 0.5 - offset[0], x=img.data_shape[1] * 0.5 - offset[1])
```
| diff --git a/nion/data/Core.py b/nion/data/Core.py
index ca5f2c4..43e17b0 100755
--- a/nion/data/Core.py
+++ b/nion/data/Core.py
@@ -386,7 +386,7 @@ def function_register_template(image_xdata: DataAndMetadata.DataAndMetadata, tem
ccorr_xdata = function_match_template(image_xdata, template_xdata)
error, ccoeff... |
nion-software__nionutils-19 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nion/utils/Converter.py:IntegerToStringConverter.convert_back"
],
"edited_modules": [
"nion/utils/Converter.py:IntegerToStringConverter"
]
},
"file": "nion/utils/Conver... | nion-software/nionutils | c4b09457ab9433dde6f224279fe8f35265c6c041 | Regex in IntegerToStringConverter not handling negative numbers
https://github.com/nion-software/nionutils/blob/c4b09457ab9433dde6f224279fe8f35265c6c041/nion/utils/Converter.py#L46
This regex is not sufficient to properly handle negative numbers. It will also fail to convert floating point numbers. See the following... | diff --git a/nion/utils/Converter.py b/nion/utils/Converter.py
index 8bfacb2..178a127 100644
--- a/nion/utils/Converter.py
+++ b/nion/utils/Converter.py
@@ -43,7 +43,7 @@ class IntegerToStringConverter(ConverterLike[int, str]):
def convert_back(self, formatted_value: typing.Optional[str]) -> typing.Optional[int]... |
nipreps__fmriprep-3025 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fmriprep/workflows/base.py:init_single_subject_wf"
],
"edited_modules": [
"fmriprep/workflows/base.py:init_single_subject_wf"
]
},
"file": "fmriprep/workflows/base.py"
... | nipreps/fmriprep | c56bec6eb7c4a39e3da929e20f16011e9a864ede | Limit fieldmap estimation to ones that will be used to correct BOLD files
### What happened?
fMRIprep uses both fmap "intended for" fmri and dwi sequences for SDC (susceptibility distortion correction, due to "Inhomogeneities of the B0 field"), instead of using only the fmap relative to fmri. The nifti file used passe... | diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 4d167248..a27a0415 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -36,12 +36,13 @@ from copy import deepcopy
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
+from niworkflows... |
nipreps__fmriprep-3369 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fmriprep/utils/bids.py:collect_derivatives"
],
"edited_modules": [
"fmriprep/utils/bids.py:collect_derivatives"
]
},
"file": "fmriprep/utils/bids.py"
}
] | nipreps/fmriprep | 73189de5ee576ffc73ab432b7419304d44ce5776 | `collect_derivatives` uses incorrect "from" entity while searching for pre-calculated boldref -> fmap coregistrations (orig vs boldref)
### What happened?
fMRIPrep generates rigid xfms between the boldref and the fieldmap that have names like `sub-{subject}_ses-{session}_task-{task}_run-{run}_from-boldref_to-{fieldmap... | diff --git a/fmriprep/data/io_spec.json b/fmriprep/data/io_spec.json
index 5d90f184..364cff7e 100644
--- a/fmriprep/data/io_spec.json
+++ b/fmriprep/data/io_spec.json
@@ -33,7 +33,7 @@
},
"boldref2anat": {
"datatype": "func",
- "from": "orig",
+ "from": "boldref",
"to": "an... |
nipreps__nibabies-351 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nibabies/utils/bids.py:Derivatives.__repr__"
],
"edited_modules": [
"nibabies/utils/bids.py:Derivatives"
]
},
"file": "nibabies/utils/bids.py"
}
] | nipreps/nibabies | 1829514594a7627a39c53cfccd7106b5173a8a6c | Proposed change to the __repr__ method of the Derivatives class
Hello,
I was peeking around the code again (debugging some issues on my side), and was trying to inspect the `Derivatives` instance created during my nibabies run.
However, the current `__repr__` method only shows attributes (with matching keys in... | diff --git a/nibabies/utils/bids.py b/nibabies/utils/bids.py
index bfd63e7..010c977 100644
--- a/nibabies/utils/bids.py
+++ b/nibabies/utils/bids.py
@@ -67,7 +67,9 @@ class Derivatives:
setattr(self, name, None)
def __repr__(self):
- return '\n'.join([name for name in self.names if getattr(se... |
nipy__heudiconv-304 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/cli/run.py:get_parser",
"heudiconv/cli/run.py:process_args"
],
"edited_modules": [
"heudiconv/cli/run.py:get_parser",
"heudiconv/cli/run.py:process_args"
... | nipy/heudiconv | 4e142b4d5332d3a65f06f460b6d99bd9543eea82 | Issues w/ slurm
Greetings,
heudiconv version 0.5.3.
I am trying to run a basic heudiconv on one subject for testing w/ slurm (running on two nodes, partition name = heudiconv) to create my heuristic.
1) Command as follows:
heudiconv -d /srv/lab/fmri/mft/dicom4bids/data/{subject}*/* -f /srv/lab/fmri/mft/... | diff --git a/heudiconv/cli/run.py b/heudiconv/cli/run.py
index 0197912..0d984fc 100644
--- a/heudiconv/cli/run.py
+++ b/heudiconv/cli/run.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
import os
import os.path as op
from argparse import ArgumentParser
@@ -215,12 +217,11 @@ def get_parser():
parser.add_argument('--... |
nipy__heudiconv-306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/dicoms.py:embed_nifti",
"heudiconv/dicoms.py:embed_metadata_from_dicoms"
],
"edited_modules": [
"heudiconv/dicoms.py:embed_nifti",
"heudiconv/dicoms.py:embe... | nipy/heudiconv | b85e5e18d6e15b36fcfa59f606eac5f3660a1143 | ERROR: Embedding failed: 'odict_values' object does not support indexing & BIDS validator
Dear Heudiconv's experts,
I have run heudiconv docker image on FDG PET data with the following command line et execution message:
```
docker run --rm -it -v /Users/mattvan83/fMRIprep/COMAJ:/data:ro -v /Users/mattvan83/fMRIpre... | diff --git a/heudiconv/dicoms.py b/heudiconv/dicoms.py
index b94013f..13a200b 100644
--- a/heudiconv/dicoms.py
+++ b/heudiconv/dicoms.py
@@ -353,7 +353,7 @@ def compress_dicoms(dicom_list, out_prefix, tempdirs, overwrite):
return outtar
-def embed_nifti(dcmfiles, niftifile, infofile, bids_info, force, min_meta... |
nipy__heudiconv-328 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "heudiconv/bids.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/cli/run.... | nipy/heudiconv | 3467341dbf50bfa813f915b3e639d62105cb9ee0 | Issues w/ slurm
Greetings,
heudiconv version 0.5.3.
I am trying to run a basic heudiconv on one subject for testing w/ slurm (running on two nodes, partition name = heudiconv) to create my heuristic.
1) Command as follows:
heudiconv -d /srv/lab/fmri/mft/dicom4bids/data/{subject}*/* -f /srv/lab/fmri/mft/... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index 40cd074..42283e6 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -11,7 +11,7 @@ import csv
from random import sample
from glob import glob
-from heudiconv.external.pydicom import dcm
+from .external.pydicom import dcm
from .parser import find_fil... |
nipy__heudiconv-354 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/convert.py:prep_conversion"
],
"edited_modules": [
"heudiconv/convert.py:prep_conversion"
]
},
"file": "heudiconv/convert.py"
}
] | nipy/heudiconv | 5357359f618a46dba7e4e55febf4e901a59f4523 | Cached heuristic name discrepancy
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
When reconverting and using a different heuristic filename from the cache, the conversion table (`filegroup.json`) is still reused. This r... | diff --git a/heudiconv/convert.py b/heudiconv/convert.py
index 73210c1..5d31b19 100644
--- a/heudiconv/convert.py
+++ b/heudiconv/convert.py
@@ -122,13 +122,21 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
# detected
# ref: https://github.com/nipy/heudiconv/issues/84#issuecomment... |
nipy__heudiconv-358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/heuristics/reproin.py:infotodict",
"heudiconv/heuristics/reproin.py:parse_series_spec"
],
"edited_modules": [
"heudiconv/heuristics/reproin.py:infotodict",
... | nipy/heudiconv | 5357359f618a46dba7e4e55febf4e901a59f4523 | Support pepolar fmaps
Not yet sure if might be reproin heuristic specific. ATM for SE sequences intended to be pepolar fieldmaps https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-4-multiple-phase-encoded-directions-pepolar we are getting files wi... | diff --git a/heudiconv/heuristics/reproin.py b/heudiconv/heuristics/reproin.py
index 4829941..e26356e 100644
--- a/heudiconv/heuristics/reproin.py
+++ b/heudiconv/heuristics/reproin.py
@@ -551,7 +551,10 @@ def infotodict(seqinfo):
if not dcm_image_iod_spec:
raise ValueError("Do not know im... |
nipy__heudiconv-376 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/bids.py:add_participant_record",
"heudiconv/bids.py:add_rows_to_scans_keys_file"
],
"edited_modules": [
"heudiconv/bids.py:add_participant_record",
"heudico... | nipy/heudiconv | fe0f2c89b96f6ee7f63d44ed3b19f004ba977c56 | Generate participants.json to accompany .tsv where fields are described
ATM we are generating `participants.tsv` with columns age, sex, group. bids-validator then whines
```
./participants.tsv
Evidence: Columns: age, sex, group not defined, please define in: /participants.json
```
We should then create/define... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index 1bbfcf6..9569278 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -240,6 +240,27 @@ def add_participant_record(studydir, subject, age, sex):
known_subjects = {l.split('\t')[0] for l in f.readlines()}
if participant_id in known_subje... |
nipy__heudiconv-379 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/utils.py:load_json"
],
"edited_modules": [
"heudiconv/utils.py:load_json"
]
},
"file": "heudiconv/utils.py"
}
] | nipy/heudiconv | d31d19d6904d59ca407f5899e405f6de4ba7d00f | enhance explicitness about what json files heudiconv fails to read
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
I was helping a user troubleshoot a problem with heudiconv, as it was tripping up on an invalid json file... | diff --git a/heudiconv/utils.py b/heudiconv/utils.py
index abea820..2453e9d 100644
--- a/heudiconv/utils.py
+++ b/heudiconv/utils.py
@@ -19,6 +19,11 @@ from nipype.utils.filemanip import which
import logging
lgr = logging.getLogger(__name__)
+if sys.version_info[0] > 2:
+ from json.decoder import JSONDecodeError... |
nipy__heudiconv-407 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/cli/run.py:process_args"
],
"edited_modules": [
"heudiconv/cli/run.py:process_args"
]
},
"file": "heudiconv/cli/run.py"
}
] | nipy/heudiconv | 536056875c111b67574e6dcf86f29c3d454d7435 | something (etelemetry?) causes logger to puke a traceback upon startup
```shell
bids@rolando:~$ heudiconv -o /tmp/cmrr -l '' --files .... -f cmrr-test.py
Traceback (most recent call last):
File "/usr/lib/python2.7/logging/__init__.py", line 868, in emit
msg = self.format(record)
File "/usr/lib/python2.7/l... | diff --git a/heudiconv/cli/run.py b/heudiconv/cli/run.py
index ed17aad..516e163 100644
--- a/heudiconv/cli/run.py
+++ b/heudiconv/cli/run.py
@@ -248,11 +248,11 @@ def process_args(args):
outdir = op.abspath(args.outdir)
- import etelemetry
try:
+ import etelemetry
latest = etelemetry.ge... |
nipy__heudiconv-424 | [
{
"changes": {
"added_entities": [
"heudiconv/convert.py:update_complex_name",
"heudiconv/convert.py:update_multiecho_name",
"heudiconv/convert.py:update_uncombined_name"
],
"added_modules": [
"heudiconv/convert.py:update_complex_name",
"heudiconv/conver... | nipy/heudiconv | 75f2850f7f07a95ff5875aba1dfd76c09e4be201 | Converting uncombined (channel-level) data
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. This includes, but is not lim... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5d4b1e2..32e72bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -360,3 +360,11 @@ TODO Summary
[#434]: https://github.com/nipy/heudiconv/issues/434
[#436]: https://github.com/nipy/heudiconv/issues/436
[#437]: https://github.com/nipy/heudiconv/issues/437
+[#425]: https:... |
nipy__heudiconv-459 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/bids.py:get_formatted_scans_key_row"
],
"edited_modules": [
"heudiconv/bids.py:get_formatted_scans_key_row"
]
},
"file": "heudiconv/bids.py"
}
] | nipy/heudiconv | f4c2dd20d4d529dbb978623b3e03c5dd79ad57be | Use AcquisitionTime for acq_time column of scans tsv files
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. This includes... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index ce8ab4c..4647358 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -404,10 +404,10 @@ def get_formatted_scans_key_row(dcm_fn):
"""
dcm_data = dcm.read_file(dcm_fn, stop_before_pixels=True, force=True)
# we need to store filenames and acquis... |
nipy__heudiconv-461 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/convert.py:update_complex_name",
"heudiconv/convert.py:update_multiecho_name",
"heudiconv/convert.py:update_uncombined_name",
"heudiconv/convert.py:save_converted_files... | nipy/heudiconv | 3f9a504270f83d00bb483c8f52ae0c228fc7d808 | Multi-echo and uncombined name updaters assume lists instead of sets
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. Thi... | diff --git a/heudiconv/convert.py b/heudiconv/convert.py
index a145732..2cbdf05 100644
--- a/heudiconv/convert.py
+++ b/heudiconv/convert.py
@@ -2,9 +2,7 @@ import filelock
import os
import os.path as op
import logging
-from math import nan
import shutil
-import sys
import random
import re
@@ -239,7 +237,7 @@ d... |
nipy__heudiconv-477 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/convert.py:update_complex_name"
],
"edited_modules": [
"heudiconv/convert.py:update_complex_name"
]
},
"file": "heudiconv/convert.py"
}
] | nipy/heudiconv | d855f64d5013f8a0e41789766a094d3c3a91552f | Replace rec entity with part entity for complex-valued data
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. This include... | diff --git a/heudiconv/convert.py b/heudiconv/convert.py
index 8e2c3c6..b88c232 100644
--- a/heudiconv/convert.py
+++ b/heudiconv/convert.py
@@ -235,7 +235,7 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
def update_complex_name(metadata, filename, suffix):
"""
- Insert `_rec-<ma... |
nipy__heudiconv-500 | [
{
"changes": {
"added_entities": [
"heudiconv/bids.py:maybe_na",
"heudiconv/bids.py:treat_age"
],
"added_modules": [
"heudiconv/bids.py:maybe_na",
"heudiconv/bids.py:treat_age"
],
"edited_entities": [
"heudiconv/bids.py:add_participant_record... | nipy/heudiconv | 6b80704e297fff859504a5df455a7f7cac88aa81 | Participants.tsv will null values
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. This includes, but is not limited to:
... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index e07c347..fc630aa 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -47,6 +47,36 @@ class BIDSError(Exception):
BIDS_VERSION = "1.4.1"
+def maybe_na(val):
+ """Return 'n/a' if non-None value represented as str is not empty
+
+ Primarily for the ... |
nipy__heudiconv-523 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/bids.py:populate_aggregated_jsons"
],
"edited_modules": [
"heudiconv/bids.py:populate_aggregated_jsons"
]
},
"file": "heudiconv/bids.py"
},
{
"changes... | nipy/heudiconv | 21d5104b0a79ac32ff8c01aa1dde3ef5b115cff2 | FileNotFoundError: [Errno 2] No such file or directory: '_task-rest_bold.json'
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as pos... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index 714e4a3..fa5d260 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -157,7 +157,7 @@ def populate_aggregated_jsons(path):
# TODO: if we are to fix it, then old ones (without _acq) should be
# removed first
task = re.sub('.*_(task... |
nipy__heudiconv-675 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/bids.py:add_participant_record",
"heudiconv/bids.py:select_fmap_from_compatible_groups"
],
"edited_modules": [
"heudiconv/bids.py:add_participant_record",
"... | nipy/heudiconv | 4383fea058e258356b09085877bf8dc63d89befb | heudiconv failure with false report of successful conversion
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. This includ... | diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index b3ff42c..f068c5a 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -6,7 +6,6 @@ __docformat__ = "numpy"
from collections import OrderedDict
import csv
-from datetime import datetime
import errno
from glob import glob
import hashlib
@@ -32,6 +31,7 @... |
nipy__heudiconv-753 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"heudiconv/dicoms.py:create_seqinfo"
],
"edited_modules": [
"heudiconv/dicoms.py:create_seqinfo"
]
},
"file": "heudiconv/dicoms.py"
}
] | nipy/heudiconv | 3eb5efa5b6852ee5a070eede43997e424527f965 | enhanced dicoms (XA) and sequence_name in PulseSequenceName dicom tag
<!-- DO NOT DELETE THIS!
This template is used to facilitate issue resolution.
All text in <!-> tags will not be displayed.
-->
### Summary
<!-- If you are having conversion troubles, please share as much
relevant information as possible. Thi... | diff --git a/heudiconv/dicoms.py b/heudiconv/dicoms.py
index 1d276e3..6210f83 100644
--- a/heudiconv/dicoms.py
+++ b/heudiconv/dicoms.py
@@ -92,6 +92,7 @@ def create_seqinfo(
image_type = get_typed_attr(dcminfo, "ImageType", tuple, ())
is_moco = "MOCO" in image_type
series_desc = get_typed_attr(dcminfo, ... |
nipy__nipy-458 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipy/algorithms/statistics/formula/formulae.py:Beta.__new__"
],
"edited_modules": [
"nipy/algorithms/statistics/formula/formulae.py:Beta"
]
},
"file": "nipy/algorithms/... | nipy/nipy | aabab7554f3b58517a894c4d43546050d9fe8864 | numpy : No module named 'numpy.testing.decorators'
for recent version of numpy (1.18.1)
```
Python 3.7.6 (default, Jan 8 2020, 19:59:22)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.12.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: from nipy.algorithms.segmentation... | diff --git a/.appveyor.yml b/.appveyor.yml
index cf72da45..15cb7438 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -10,12 +10,12 @@ environment:
- PYTHON: C:\Python27-x64
# Doctest fail from the long Ls, as in (1L, 2L) != (1, 2)
EXTRA_FLAGS: "--without-doctest"
- - PYTHON: C:\Python34
- - PY... |
nipy__nipype-1937 | [
{
"changes": {
"added_entities": [
"nipype/interfaces/utility/base.py:_ravel"
],
"added_modules": [
"nipype/interfaces/utility/base.py:_ravel"
],
"edited_entities": [
"nipype/interfaces/utility/base.py:Merge.__init__",
"nipype/interfaces/utility/base... | nipy/nipype | d68b929ae1f36f2704fa7cddd029b308acf8587a | New behaviour of Merge interface with breaks generic cases where numinputs=1 at runtime
### Summary
In the current HEAD, the new behaviour of the Merge interface when `numinputs==1` breaks cases (such as mine) where the `numinputs` is set at runtime depending on parameters of the workflow creation code. A better way... | diff --git a/nipype/interfaces/utility/base.py b/nipype/interfaces/utility/base.py
index 45261c998..03442df20 100644
--- a/nipype/interfaces/utility/base.py
+++ b/nipype/interfaces/utility/base.py
@@ -99,13 +99,29 @@ class IdentityInterface(IOBase):
class MergeInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
... |
nipy__nipype-2019 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/pipeline/engine/nodes.py:MapNode._make_nodes"
],
"edited_modules": [
"nipype/pipeline/engine/nodes.py:MapNode"
]
},
"file": "nipype/pipeline/engine/nodes.py"
}... | nipy/nipype | 4358fe5d10b22c036b4c2f3d7cf99d20d88d76ec | Processes in MapNodes do not respect thread limits
### Summary
If a `MapNode`'s interface is assigned a `num_threads` greater than half of the available threads, the jobs may nonetheless run in parallel.
### Expected behavior
Such jobs ought to run one at a time.
### How to replicate the behavior
The fol... | diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py
index cbfa70ceb..d52e589a0 100644
--- a/nipype/pipeline/engine/nodes.py
+++ b/nipype/pipeline/engine/nodes.py
@@ -1112,9 +1112,14 @@ class MapNode(Node):
nitems = len(filename_to_list(getattr(self.inputs, self.iterfield[0])))
... |
nipy__nipype-2030 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/spm/model.py:EstimateModel._format_arg",
"nipype/interfaces/spm/model.py:EstimateModel._parse_inputs",
"nipype/interfaces/spm/model.py:EstimateModel._list_outputs"
... | nipy/nipype | cda3fdc3be231f2c9d7bdbdbadee472a0bad9e92 | spm.EstimateModel additional args broken
### Summary
Issue brought up on [Neurostars#436](https://neurostars.org/t/nipype-interfaces-without-options-present-in-the-underlying-executable-function/436)
### Actual behavior
`EstimateModel` expects a string for input `flags`, but later expects a dictionary.
### Expected... | diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
index 4a55a4ea7..ddf35ef44 100644
--- a/nipype/interfaces/spm/model.py
+++ b/nipype/interfaces/spm/model.py
@@ -29,7 +29,7 @@ from ...utils.filemanip import (filename_to_list, list_to_filename,
from ..base import (Bunch, traits, TraitedSpec, ... |
nipy__nipype-2031 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/freesurfer/preprocess.py:BBRegister._list_outputs",
"nipype/interfaces/freesurfer/preprocess.py:BBRegister._format_arg"
],
"edited_modules": [
"nipype/inter... | nipy/nipype | 90cfdd8a63114dbe2e1ce6dea9dd739d04f84a4a | bbregister api: new version allows saving to lta (preferred) | diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
index 0ff32ad74..4e164c342 100644
--- a/nipype/interfaces/freesurfer/preprocess.py
+++ b/nipype/interfaces/freesurfer/preprocess.py
@@ -1155,6 +1155,8 @@ class BBRegisterInputSpec(FSTraitedSpec):
... |
nipy__nipype-2065 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/mipav/developer.py:JistIntensityMp2rageMaskingInputSpec"
]
},
"file": "nipype/interfaces/mipav/developer.py"
}
] | nipy/nipype | a63c52d97df65d316a5c97a40dd9c7e5a63d237c | JistIntensityMp2rageMasking interface incompatible with current CBS Tools release
For the command underlying the interface mipav.JistIntensityMp2rageMasking the parameter names have changed in the current CBS Tools release, which makes the interface fail. I meant to do a PR but then saw the mipav/developer.py file is a... | diff --git a/README.rst b/README.rst
index aa41f34d6..5064198dd 100644
--- a/README.rst
+++ b/README.rst
@@ -33,7 +33,7 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
.. image:: https://img.shields.io/badge/gitter-join%20chat%20%E2%86%92-brightgreen.svg?style=flat
:target: http://gitter.im/nipy/nipyp... |
nipy__nipype-2139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/base.py:MultiPath.validate"
],
"edited_modules": [
"nipype/interfaces/base.py:MultiPath"
]
},
"file": "nipype/interfaces/base.py"
}
] | nipy/nipype | d9b183b046815e836ce285eab894928c8849b27c | iterfield in MapNode can't be range (py3)
### Summary
In py3 `range` is not a list, and if iterfield in `MapNode` is defined as `range` than entire range is send to the interface at once.
### Script/Workflow details
```
from nipype import Function, MapNode
def square_func(x):
print(x, type(x))
re... | diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py
index 2f8b1bf0e..19cf9ccaa 100644
--- a/nipype/interfaces/base.py
+++ b/nipype/interfaces/base.py
@@ -32,6 +32,7 @@ from warnings import warn
import simplejson as json
from dateutil.parser import parse as parseutc
from packaging.version import Versio... |
nipy__nipype-2179 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/afni/utils.py:CatMatvecInputSpec"
]
},
"file": "nipype/interfaces/afni/utils.py"
}
] | nipy/nipype | 7ead69d1aeb24f0d0884efe03075ef7de1759e1c | typo in trait name of AFNI CatMatvec interface
### Summary
typo in `afni.Catmatvec`: trait name is `fourxfour` not `fourXfour`
https://github.com/nipy/nipype/blob/master/nipype/interfaces/afni/utils.py#L610
### Actual behavior
```Python
from nipype.interfaces import afni
cat_matvec = afni.CatMatvec()
cat_mat... | diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
index e20fe1d5f..88a317b8c 100644
--- a/nipype/interfaces/afni/utils.py
+++ b/nipype/interfaces/afni/utils.py
@@ -602,12 +602,12 @@ class CatMatvecInputSpec(AFNICommandInputSpec):
"This feature could be used, with clever scri... |
nipy__nipype-2349 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/io.py:FSSourceInputSpec"
]
},
"file": "nipype/interfaces/io.py"
}
] | nipy/nipype | 045b28ef9056fac1107bc4f0707859d043f3bfd1 | FreeSurferSource doesn't check subjects_dir
### Summary
`FreeSurferSource` doesn't check `subjects_dir` is an existing path.
### How to replicate the behavior
```
from nipype.interfaces.io import FreeSurferSource
fs = FreeSurferSource()
fs.inputs.subjects_dir = 'path/to/no/existing/directory'
fs.inputs.subje... | diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index fc3617036..6bb9a943f 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -1555,16 +1555,12 @@ class DataFinder(IOBase):
class FSSourceInputSpec(BaseInterfaceInputSpec):
- subjects_dir = Directory(
- mandatory=True, des... |
nipy__nipype-2363 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/utils/config.py:NipypeConfig.get_display"
],
"edited_modules": [
"nipype/utils/config.py:NipypeConfig"
]
},
"file": "nipype/utils/config.py"
}
] | nipy/nipype | f3b09125eceec7b90ad801176892aab06e012f8c | issue with MIPAV module
Dear all,
I've tried to run the example on MP2RAGE-skullstripping http://nipype.readthedocs.io/en/latest/users/examples/smri_cbs_skullstripping.html with nipype 0.14.0 and CBStools version 3.0. I use a conda environment based on python 2.7.
Here is the error message:
Traceback:
Traceback... | diff --git a/CHANGES b/CHANGES
index fa1716688..8dcca2ba6 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,6 +1,7 @@
Upcoming release (0.14.1)
=========================
+* FIX: Errors parsing ``$DISPLAY`` (https://github.com/nipy/nipype/pull/2363)
* FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/ni... |
nipy__nipype-2429 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/mrtrix3/preprocess.py:ResponseSDInputSpec"
]
},
"file": "nipype/interfaces/mrtrix3/preprocess.py"
}
] | nipy/nipype | 168dfee8862e3a635d8fd6f0f4469ad0950e55b9 | Mrtrix3 `dwi2response` - bad algorithm argument position
### Summary
Th Mrtrix3 `dwi2response` CL wrapper generates the following runtime error:
```shell
dwi2response:
mrinfo: [ERROR] no diffusion encoding information found in image "<DWI_FILE>"
dwi2response: [ERROR] Script requires diffusion gradient table: eit... | diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index ca5996bea..740513194 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -27,7 +27,7 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
'tournier',
't... |
nipy__nipype-2432 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/pipeline/engine/base.py:EngineBase.clone"
],
"edited_modules": [
"nipype/pipeline/engine/base.py:EngineBase"
]
},
"file": "nipype/pipeline/engine/base.py"
}
] | nipy/nipype | d7a8085d9230c4f43489ba93742ea1f6401f3ede | workflow with iterables and cloned nodes fail when expanding iterables
### Summary
When running a workflow which includes a cloned node and iterables the workflow will fail when expanding the iterables because the id of the cloned node will be the same as the original one.
### Actual behavior
Will result in an err... | diff --git a/nipype/pipeline/engine/base.py b/nipype/pipeline/engine/base.py
index 51449632b..0883023f6 100644
--- a/nipype/pipeline/engine/base.py
+++ b/nipype/pipeline/engine/base.py
@@ -84,9 +84,12 @@ class EngineBase(object):
A clone of node or workflow must have a new name
"""
if nam... |
nipy__nipype-2471 | [
{
"changes": {
"added_entities": [
"nipype/interfaces/niftyreg/regutils.py:RegTools._format_arg"
],
"added_modules": null,
"edited_entities": [
"nipype/interfaces/niftyreg/regutils.py:RegResample._format_arg"
],
"edited_modules": [
"nipype/interfaces/n... | nipy/nipype | 6ca791d9c5ec0efb9f56cc9e44758d6e53ffb800 | NiftyReg's RegTools is missing interpolation order argument | diff --git a/.zenodo.json b/.zenodo.json
index 1058e3b15..29e7f047a 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -558,7 +558,7 @@
"name": "Flandin, Guillaume"
},
{
- "affiliation": "Stereotaxy Core, Brain & Spine Institute",
+ "affiliation": "University College London",
"name": "P\u... |
nipy__nipype-2479 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/pipeline/engine/utils.py:generate_expanded_graph"
],
"edited_modules": [
"nipype/pipeline/engine/utils.py:generate_expanded_graph"
]
},
"file": "nipype/pipeline/... | nipy/nipype | e6792158568a51f0e6cdef77c6ca12ab6266a7dd | Issue with node name that starts with another node's name
I think the [line ~801 in util.py](https://github.com/nipy/nipype/edit/master/nipype/pipeline/engine/utils.py#L801) should be something like this:
for node in graph_in.nodes():
for src_id, edge_data in list(old_edge_dict.items()):... | diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index 2b6bb6ed3..301a35844 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -1050,7 +1050,17 @@ def generate_expanded_graph(graph_in):
expansions = defaultdict(list)
for node in ... |
nipy__nipype-2490 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/utils/nipype2boutiques.py:generate_boutiques_descriptor",
"nipype/utils/nipype2boutiques.py:create_tempfile",
"nipype/utils/nipype2boutiques.py:must_generate_value"
],
... | nipy/nipype | 88dbce1ce5439440bcc14c9aa46666c40f642152 | UnboundLocalError: local variable 'module_name' referenced before assignment
### Summary
Discovered for myself `nipypecli` and decided to give it a try while composing cmdline invocation just following the errors it was spitting out at me and stopping when error didn't give a hint what I could have specified incorrect... | diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 9f228f5c5..21ecbc0ee 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -2,7 +2,7 @@
from __future__ import (print_function, division, unicode_literals,
absolute_import)
... |
nipy__nipype-2502 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/afni/preprocess.py:Allineate._format_arg",
"nipype/interfaces/afni/preprocess.py:Allineate._list_outputs",
"nipype/interfaces/afni/preprocess.py:Allineate._gen_filename... | nipy/nipype | 27b33ef128f761cc7166205fc42ef7c04a8d4e4f | issues with afni.allineate w/ solution (and possible issue with genfile parameter)
### Summary
Hi all. Just started learning nipype, and it's been pretty great so far. I've only run into issues with the `afni.allineate` interface. I was able to fix it on my own, but I thought I should post an issue here for awarene... | diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
index 13a065c27..9ede8d13e 100644
--- a/nipype/interfaces/afni/preprocess.py
+++ b/nipype/interfaces/afni/preprocess.py
@@ -218,7 +218,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
out_file = File(
desc='output... |
nipy__nipype-2527 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/afni/utils.py:CatMatvecInputSpec"
]
},
"file": "nipype/interfaces/afni/utils.py"
}
] | nipy/nipype | e446466290b9ccba5d5aa589971c97e744d9267b | AFNI CatMatvec: Caching fails and output file undefined
### Summary
AFNI CatMatvec interface caching fails and output file is undefined
### How to replicate the behavior
```Python
from nipype.interfaces import afni
from nipype.caching import Memory
memory = Memory('/tmp/test_catmatvec/')
catmatvec = memory.cach... | diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
index 9f306c7b8..cb01ae4a2 100644
--- a/nipype/interfaces/afni/utils.py
+++ b/nipype/interfaces/afni/utils.py
@@ -564,8 +564,11 @@ class CatMatvecInputSpec(AFNICommandInputSpec):
argstr="%s",
position=-2)
out_file = Fi... |
nipy__nipype-2595 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/utils/config.py:NipypeConfig.enable_debug_mode"
],
"edited_modules": [
"nipype/utils/config.py:NipypeConfig"
]
},
"file": "nipype/utils/config.py"
}
] | nipy/nipype | 9eaa2a32c8cb3569633a79d6f7968270453f9aed | config.enable_debug_mode() does not work as advertised
config.enable_debug_mode() is not equivalent to:
```
mkdir ~/.nipype
echo "[logging]" > ~/.nipype/nipype.cfg
echo "workflow_level = DEBUG" ~/.nipype/nipype.cfg
echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg
echo "filemanip_level = DEBUG" >> ~/.nipype/nipyp... | diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst
index 279dc1aad..8d296556c 100644
--- a/doc/users/config_file.rst
+++ b/doc/users/config_file.rst
@@ -237,16 +237,23 @@ Debug configuration
To enable debug mode, one can insert the following lines::
- from nipype import config, logging
+ from nip... |
nipy__nipype-2597 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/pipeline/engine/utils.py:generate_expanded_graph"
],
"edited_modules": [
"nipype/pipeline/engine/utils.py:generate_expanded_graph"
]
},
"file": "nipype/pipeline/... | nipy/nipype | 9eaa2a32c8cb3569633a79d6f7968270453f9aed | PR #2479 has broken my package
### Summary
PR #2479 has broken my package (https://pypi.org/project/arcana/)
I am not quite sure what the rationale behind the changes are so it is difficult to know how to debug or whether there is something I can change in my package.
### Actual behavior
Workflow exits wit... | diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index 08d357ff6..0a59aac26 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -1054,12 +1054,14 @@ def generate_expanded_graph(graph_in):
for src_id in list(old_edge_dict.keys()):
... |
nipy__nipype-2628 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/fsl/dti.py:FSLXCommandInputSpec"
]
},
"file": "nipype/interfaces/fsl/dti.py"
}
] | nipy/nipype | 7ea4f1bd3e99a276ea99423a2534a68556e036c7 | Wrong argstr for fsl:bedpostx
### Summary
File fsl/dti.py, Line 174:
An argument "burninnoard" for bedpostx is set. This argument does not exist, bedpostx crashes.
The correct argument is "burnin_noard".
### Solution
Please change
argstr='--burninnoard=%d',
to
argstr='--burnin_noard=%d', | diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py
index f318b5cb1..d8812cec6 100644
--- a/nipype/interfaces/fsl/dti.py
+++ b/nipype/interfaces/fsl/dti.py
@@ -171,7 +171,7 @@ class FSLXCommandInputSpec(FSLCommandInputSpec):
low=0,
value=0,
usedefault=True,
- argst... |
nipy__nipype-2669 | [
{
"changes": {
"added_entities": [
"nipype/pipeline/engine/base.py:EngineBase.itername",
"nipype/pipeline/engine/base.py:EngineBase.__repr__"
],
"added_modules": null,
"edited_entities": [
"nipype/pipeline/engine/base.py:EngineBase.__init__"
],
"edited... | nipy/nipype | 69dce12bdf256c3bb0a8b6da9a1d1cdce48b66ec | incorrect detailed graphs being generated
### Summary
the detailed graph is not listing names of nodes appropriately resulting in incorrect graphs.
scroll down to see the multiple arrows containing nodes in the figures of the following notebook.
https://miykael.github.io/nipype_tutorial/notebooks/introduction_qu... | diff --git a/nipype/pipeline/engine/base.py b/nipype/pipeline/engine/base.py
index 9d0bc3c69..7f7afd392 100644
--- a/nipype/pipeline/engine/base.py
+++ b/nipype/pipeline/engine/base.py
@@ -36,11 +36,11 @@ class EngineBase(object):
"""
self._hierarchy = None
- self._name = None
+ self.n... |
nipy__nipype-2673 | [
{
"changes": {
"added_entities": [
"nipype/pipeline/engine/utils.py:_identify_collapses",
"nipype/pipeline/engine/utils.py:_uncollapse",
"nipype/pipeline/engine/utils.py:_protect_collapses"
],
"added_modules": [
"nipype/pipeline/engine/utils.py:_identify_collaps... | nipy/nipype | 69dce12bdf256c3bb0a8b6da9a1d1cdce48b66ec | Node de-listifies output lists with a single element
### Summary / Actual behavior
A `Select` interface can return a single-element list, when that is the element selected. However, if placed in a `Node`, this will be unwrapped and the output will be the element itself.
### Expected behavior
`Node` should not ... | diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index 4ec36afe6..cc47de5d4 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -233,15 +233,78 @@ def write_report(node, report_type=None, is_mapnode=False):
return
+def _identify_collapses(hastrait... |
nipy__nipype-2749 | [
{
"changes": {
"added_entities": [
"nipype/interfaces/ants/segmentation.py:LaplacianThickness._gen_filename",
"nipype/interfaces/ants/segmentation.py:LaplacianThickness._list_outputs"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"ni... | nipy/nipype | a10963c408d3e3bbc8e1e91a21a7779ee2ca3fe9 | FSL dtifit add sse to outputspec
### Summary
nipype's interface for FSL dtifit currently has a parameter "sse" which produces the sum of squared errors. This output does not appear in the OutputSpec.
### Actual behavior
You can use the parameter and the image is produced correctly, but there is no way to further c... | diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py
index 04d212ec0..b0ce64764 100644
--- a/nipype/interfaces/ants/segmentation.py
+++ b/nipype/interfaces/ants/segmentation.py
@@ -203,9 +203,7 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
desc='name of out... |
nipy__nipype-2750 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/fsl/epi.py:Eddy._list_outputs"
],
"edited_modules": [
"nipype/interfaces/fsl/epi.py:EddyInputSpec",
"nipype/interfaces/fsl/epi.py:EddyOutputSpec",
"... | nipy/nipype | 1eeabd36597b67b192d6e16fd3abbb8d1d8121bf | Additional parameters for FSL Eddy
### Summary
nipype's interface for FSL eddy currently does not support the parameters "--cnr_maps" and "--residuals".
### Actual behavior
You can use the parameters through the args string, but then you can not connect the resulting output to other nodes!
### Expected behavio... | diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
index 84bd9e8db..a13da0e0d 100644
--- a/nipype/interfaces/fsl/epi.py
+++ b/nipype/interfaces/fsl/epi.py
@@ -659,6 +659,10 @@ class EddyInputSpec(FSLCommandInputSpec):
"the field specified by --field and first volume "
"in file --... |
nipy__nipype-2757 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "nipype/info.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/mes... | nipy/nipype | 2995ded211a325aafcf7832f7799efe8b8e781c7 | 'MeshFixInputSpec' object has no attribute 'save_as_vrml'
### Summary
Hi, I'm a newbie and am currently trying to revive a [4 years old repository](https://github.com/CyclotronResearchCentre/forward). This code makes use of MeshFix interface. When running an example I get an `AttributeError`.
### Actual behavior
... | diff --git a/nipype/info.py b/nipype/info.py
index 936c6b63e..5efb4282b 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -108,7 +108,7 @@ DATEUTIL_MIN_VERSION = '2.2'
PYTEST_MIN_VERSION = '3.0'
FUTURE_MIN_VERSION = '0.16.0'
SIMPLEJSON_MIN_VERSION = '3.8.0'
-PROV_VERSION = '1.5.2'
+PROV_VERSION = '1.5.0'
CLICK_MI... |
nipy__nipype-2780 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/meshfix.py:MeshFixInputSpec"
]
},
"file": "nipype/interfaces/meshfix.py"
}
] | nipy/nipype | e4753317288bc3440b28fa30da1c680187d7b07b | Meshfix interface inverting command parameters
### Summary
Hi,
While using the MeshFix interface, I received this error:
```shell
RuntimeError: Command:
meshfix /path/to/file.off -a 2.000000 0.200000 --fineTuneIn 4 --shells 2 -o file_fixed.off -q
Standard output:
Fixing asin tolerance to 3.491368e-02
Standard ... | diff --git a/.zenodo.json b/.zenodo.json
index 1a7ba4632..2c92959ec 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -587,6 +587,11 @@
"affiliation": "MIT, HMS",
"name": "Ghosh, Satrajit",
"orcid": "0000-0002-5312-6729"
+ },
+ {
+ "affiliation": "GIGA Institute",
+ "name": "Grignard,... |
nipy__nipype-3637 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nipype/interfaces/utility/csv.py:CSVReader._parse_line",
"nipype/interfaces/utility/csv.py:CSVReader._get_outfields",
"nipype/interfaces/utility/csv.py:CSVReader._list_outputs"
],
... | nipy/nipype | c46a957bdfa2e573fb9da3c5a867046a0153f56a | CSVReader does not handle quoted fields or tsv files
### Summary
I want to add functionality to the CSVReader so it can handle tsv files. While checking that out, I noticed that we're just splitting on `,`, which is not ideal.
### Actual behavior
Parsing CSV files with fields that contain quoted text with ',' char... | diff --git a/nipype/interfaces/utility/csv.py b/nipype/interfaces/utility/csv.py
index 3bfc46203..da09e425f 100644
--- a/nipype/interfaces/utility/csv.py
+++ b/nipype/interfaces/utility/csv.py
@@ -2,6 +2,7 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""CSV Handling utilities
"""
+import csv
from ..base import traits... |
nipy__nipype-3658 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/mrtrix3/utils.py:Generate5ttInputSpec"
]
},
"file": "nipype/interfaces/mrtrix3/utils.py"
}
] | nipy/nipype | e03ab6f99f85fb54bc5f1ed2d9222af8f5bd66e0 | [ENH] Enhance implementation of 5ttgen
### Summary
Current implementation lacks some inputs that are available through the original command ([MRTrix3's `5ttgen`](https://mrtrix.readthedocs.io/en/dev/reference/commands/5ttgen.html))
### Actual behavior
Currently only `in_file`, `algorithm` and `out_file` are availabl... | diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 7e25288d1..8a69232ec 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -241,6 +241,49 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
desc="input image / directory",
)
... |
nipy__nipype-3663 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nipype/interfaces/mrtrix3/utils.py:TensorMetricsInputSpec"
]
},
"file": "nipype/interfaces/mrtrix3/utils.py"
}
] | nipy/nipype | 6ac81cabddcd1174e1d8630737136aa14b4a11ed | [BUG] TensorToMetrics inputs specification doesn't inherit from Mrtrix3 Base
### Summary
The TensorMetricsInputSpec doesn't inherit from MRTrix3BaseInputSpec, making some of the basic inputs unavailable for this class.
### Actual behavior
The specifications inherit from the CommandLineInputSpec.
### Expected be... | diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 8a69232ec..1a7c81dad 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -318,7 +318,7 @@ class Generate5tt(MRTrix3Base):
return outputs
-class TensorMetricsInputSpec(CommandLi... |
nipy__nitime-189 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nitime/analysis/coherence.py:MTCoherenceAnalyzer.df",
"nitime/analysis/coherence.py:MTCoherenceAnalyzer.weights"
],
"edited_modules": [
"nitime/analysis/coherence.py:MTCohere... | nipy/nitime | 5d44b0bca126a6bc14d39fbd33cbdbf14edc3a2c | nitime.analysis.coherence.MTCoherenceAnalyzer causing an error when fed with bandwidth parameter
Greetings,
I have noisy vascular measurements acquired at 30Hz for 89 seconds. I'd like to inspect their multi-taper coherence in the 0.1-2.5Hz range, as done in [1]. In particular, I'd like to use an increased bandwidth... | diff --git a/nitime/analysis/coherence.py b/nitime/analysis/coherence.py
index ab577e1..903c1a6 100644
--- a/nitime/analysis/coherence.py
+++ b/nitime/analysis/coherence.py
@@ -304,7 +304,7 @@ class MTCoherenceAnalyzer(BaseAnalyzer):
@desc.setattr_on_read
def df(self):
# The degrees of freedom:
- ... |
nipy__nitime-221 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "nitime/index_utils.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nitime/timeser... | nipy/nitime | 696b83424739dd958c0d36f3804c43fc1a9a7271 | numpy 2.0 compatibility
https://github.com/conda-forge/nitime-feedstock/pull/32 indicates (unsurprisingly) that there are numpy 2.0 compatibilities.
With numpy 2.0 in RC phase, it's probably time to try to fix these.
I don't have the time at the moment, unfortunately. | diff --git a/nitime/algorithms/event_related.py b/nitime/algorithms/event_related.py
index acf7d34..e0141a3 100644
--- a/nitime/algorithms/event_related.py
+++ b/nitime/algorithms/event_related.py
@@ -10,7 +10,7 @@ from nitime.lazy import scipy_fftpack as fftpack
def fir(timeseries, design):
- """
+ r"""
... |
nipype__pydra-186 | [
{
"changes": {
"added_entities": [
"pydra/engine/core.py:is_lazy"
],
"added_modules": [
"pydra/engine/core.py:is_lazy"
],
"edited_entities": [
"pydra/engine/core.py:TaskBase.checksum_states",
"pydra/engine/core.py:TaskBase.done"
],
"edite... | nipype/pydra | 6d6340500696f68390de551bd168b54d3f88dc21 | TODO for Shell Task and ContainerTask
There are some issues tak don't have to be fixed right away, but should be done soon:
(will be updated)
- [x] cmdline for Shell: doesn't make sense for tasks with splitter
- [x] inputs for Containers:
- checking if has image and it's proper image, raising exceptions;... | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index 11111396..7cd8b7b8 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -247,9 +247,9 @@ class TaskBase:
TODO
"""
+ self.state.prepare_states(self.inputs)
+ self.state.prepare_inputs()
if state_index... |
nipype__pydra-211 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/core.py:TaskBase._run"
],
"edited_modules": [
"pydra/engine/core.py:TaskBase"
]
},
"file": "pydra/engine/core.py"
},
{
"changes": {
"added_en... | nipype/pydra | 73ac9828d1e0a81720907cf2d518cafea34afba9 | template_update does not take type of value into account
the `template_update` function cannot simply check for equality of objects.
https://github.com/nipype/pydra/blob/master/pydra/engine/helpers_file.py#L508
<summary>
Code
<details>
```
import numpy as np
fft = pydra.mark.annotate({'a': np.ndarray, 'retu... | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index 5e3e8efe..e630588a 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -381,7 +381,7 @@ class TaskBase:
orig_inputs = attr.asdict(self.inputs)
map_copyfiles = copyfile_input(self.inputs, self.output_dir)
mo... |
nipype__pydra-213 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/helpers_state.py:input_shape",
"pydra/engine/helpers_state.py:splits",
"pydra/engine/helpers_state.py:_single_op_splits",
"pydra/engine/helpers_state.py:map_splits"
... | nipype/pydra | 81af3b872a22e57f02c62d4107528231170ca467 | State changes: adding container_dim concept
We want to add an optional argument to the `split` that specify the dimension of the "container" that will be used for splitting. This is important to be able to recognize what is the dimension of container and what is the dimension of the object that should be passed to th... | diff --git a/pydra/engine/helpers_state.py b/pydra/engine/helpers_state.py
index 65a580de..8136e2a1 100644
--- a/pydra/engine/helpers_state.py
+++ b/pydra/engine/helpers_state.py
@@ -362,14 +362,15 @@ def iter_splits(iterable, keys):
yield dict(zip(keys, list(flatten(iter, max_depth=1000))))
-def input_sha... |
nipype__pydra-217 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/helpers.py:make_klass"
],
"edited_modules": [
"pydra/engine/helpers.py:make_klass"
]
},
"file": "pydra/engine/helpers.py"
}
] | nipype/pydra | 7ceb4def20a07d7e4394ea69aed32ca376e14f73 | Readable SpecInfos
The SpecInfo class is currently very inscrutable. An improved `__repr__` will be important for making development more friendly. | diff --git a/pydra/engine/helpers.py b/pydra/engine/helpers.py
index 4835dfe9..1a441f1d 100644
--- a/pydra/engine/helpers.py
+++ b/pydra/engine/helpers.py
@@ -221,13 +221,29 @@ def make_klass(spec):
if isinstance(item[1], attr._make._CountingAttr):
newfields[item[0]] = item[1]
... |
nipype__pydra-221 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/helpers_file.py:fname_presuffix",
"pydra/engine/helpers_file.py:get_related_files"
],
"edited_modules": [
"pydra/engine/helpers_file.py:fname_presuffix",
... | nipype/pydra | bba381dbd60a13b148975ff853f25a13f29da970 | updating pydra for windows machine | diff --git a/pydra/engine/helpers_file.py b/pydra/engine/helpers_file.py
index 8014d43c..065986e3 100644
--- a/pydra/engine/helpers_file.py
+++ b/pydra/engine/helpers_file.py
@@ -91,6 +91,8 @@ def fname_presuffix(fname, prefix="", suffix="", newpath=None, use_ext=True):
Examples
--------
+ >>> import pyt... |
nipype__pydra-222 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/helpers.py:hash_value"
],
"edited_modules": [
"pydra/engine/helpers.py:hash_value"
]
},
"file": "pydra/engine/helpers.py"
}
] | nipype/pydra | 349d954add42e4297ce127c2fa61f49346cc19a1 | review what should be included checksum
for example I'm removing bindings and input that have output_file_template | diff --git a/pydra/engine/helpers.py b/pydra/engine/helpers.py
index 1a441f1d..3cd9c65a 100644
--- a/pydra/engine/helpers.py
+++ b/pydra/engine/helpers.py
@@ -10,7 +10,7 @@ from hashlib import sha256
import subprocess as sp
from .specs import Runtime, File, attr_fields
-from .helpers_file import is_existing_file, h... |
nipype__pydra-255 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/helpers_file.py:is_existing_file"
],
"edited_modules": [
"pydra/engine/helpers_file.py:is_existing_file"
]
},
"file": "pydra/engine/helpers_file.py"
}
] | nipype/pydra | acc90101af22637ff71139224441eacd08b14452 | error returning numpy arrays with more than one element in workflow output
version: pydra master
the key piece appears to be the fact that a numpy array is being returned with more than 1 element. i.e the error goes away if the output of the function is changed to `np.array([val])` or `np.array([val, val]).tolist()`... | diff --git a/pydra/engine/helpers_file.py b/pydra/engine/helpers_file.py
index f15e2028..39f38785 100644
--- a/pydra/engine/helpers_file.py
+++ b/pydra/engine/helpers_file.py
@@ -535,11 +535,11 @@ def is_local_file(f):
return f.type is File and "container_path" not in f.metadata
-def is_existing_file(f):
+def ... |
nipype__pydra-261 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/task.py:FunctionTask._run_task"
],
"edited_modules": [
"pydra/engine/task.py:FunctionTask"
]
},
"file": "pydra/engine/task.py"
}
] | nipype/pydra | 0067eeee42a8db39a80653e3821056c6ad87ead2 | Task crashes when function returns None
in both cases the named outputs should be set to `None`.
```
import pydra
import typing as ty
import os
@pydra.mark.task
@pydra.mark.annotate({"return": {"b": ty.Any}})
def test_multiout(val, val2):
return None
if __name__ == "__main__":
cache_dir = os... | diff --git a/pydra/engine/task.py b/pydra/engine/task.py
index 8cb088a2..d8aaa60d 100644
--- a/pydra/engine/task.py
+++ b/pydra/engine/task.py
@@ -199,19 +199,21 @@ class FunctionTask(TaskBase):
del inputs["_func"]
self.output_ = None
output = cp.loads(self.inputs._func)(**inputs)
- if... |
nipype__pydra-315 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/core.py:TaskBase._collect_outputs"
],
"edited_modules": [
"pydra/engine/core.py:TaskBase"
]
},
"file": "pydra/engine/core.py"
},
{
"changes": {
... | nipype/pydra | 50051730c4bf894ce9ba4833f8c267b5993e0ce0 | fixing file naming in output_file_template
When file name with extension is modified in `output_file_template` the name is not modified correctly, see e.g. [test_wf_shell_cmd_3](https://github.com/nipype/pydra/blob/master/pydra/engine/tests/test_shelltask.py#L1646).
The result, `res.output.cp_file`, is `.../newfile.t... | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index 844df5ce..ec628760 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -423,9 +423,7 @@ class TaskBase:
self.output_spec = output_from_inputfields(self.output_spec, self.inputs)
output_klass = make_klass(self.output_spec)
... |
nipype__pydra-344 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/core.py:TaskBase.output_names",
"pydra/engine/core.py:TaskBase._run",
"pydra/engine/core.py:TaskBase._collect_outputs",
"pydra/engine/core.py:Workflow.set_output"
... | nipype/pydra | 79573fde5a43a5cdff714b819f2b49185d8f85c9 | More issues with numpy arrays
Still having errors with comparing arrays, now in `copyfile_workflow`. It's somewhat confusing that `value` can be the actual output or the path to output file.
Error:
```python
---------------------------------------------------------------------------
ValueError ... | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index b04a50ea..90bd3d34 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -34,7 +34,6 @@ from .helpers import (
ensure_list,
record_error,
hash_function,
- output_from_inputfields,
)
from .helpers_file import copyfile_input, tem... |
nipype__pydra-573 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/core.py:Workflow.__init__"
],
"edited_modules": [
"pydra/engine/core.py:Workflow"
]
},
"file": "pydra/engine/core.py"
}
] | nipype/pydra | 219c72170984f013eeb1fdc3d87f1d4a58d0dfab | `Workflow` constructor raises `TypeError` when `input_spec` is an instance of `SpecInfo`
The documentation of the `Workflow` constructor says that `input_spec` can be a list of strings, a `SpecInfo`, or a `BaseSpec` instance:
https://github.com/nipype/pydra/blob/219c72170984f013eeb1fdc3d87f1d4a58d0dfab/pydra/engine/... | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index 42b78054..b66549e2 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -843,6 +843,12 @@ class Workflow(TaskBase):
if input_spec:
if isinstance(input_spec, BaseSpec):
self.input_spec = input_spec
+ ... |
nipype__pydra-614 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/task.py:ShellCommandTask._command_pos_args",
"pydra/engine/task.py:split_cmd"
],
"edited_modules": [
"pydra/engine/task.py:ShellCommandTask",
"pydra/engi... | nipype/pydra | a9a116d886fd9263ade5fcf4a3fb2a73d1676064 | Proper way to format a tuple parameter
I have got an interface which expects a parameter `foo` as a triple with the following format `--foo 1 2 3`
I reached for the following definition as a first attempt:
```python
input_spec = pydra.specs.SpecInfo(
name="Input",
fields=[
(
"foo"... | diff --git a/pydra/engine/task.py b/pydra/engine/task.py
index 135af507..f808c037 100644
--- a/pydra/engine/task.py
+++ b/pydra/engine/task.py
@@ -371,7 +371,7 @@ class ShellCommandTask(TaskBase):
return value
def _command_shelltask_executable(self, field):
- """Returining position and value for ... |
nipype__pydra-71 | [
{
"changes": {
"added_entities": [
"pydra/engine/core.py:Workflow.create_connections"
],
"added_modules": null,
"edited_entities": [
"pydra/engine/core.py:Workflow.__init__",
"pydra/engine/core.py:Workflow.add",
"pydra/engine/core.py:Workflow._run"
]... | nipype/pydra | 71cfc9f2c6cfeffa2714804e6bbf4a67b0167b7e | edges not created if input set after `wf.add`
see the xfailing `test_wf_2b`: https://github.com/nipype/pydra/blob/master/pydra/engine/tests/test_workflow.py#L95
compare with `test_wf_2` and `test_wf_2a` | diff --git a/pydra/engine/core.py b/pydra/engine/core.py
index f5c8c931..c2f05697 100644
--- a/pydra/engine/core.py
+++ b/pydra/engine/core.py
@@ -462,7 +462,6 @@ class Workflow(TaskBase):
# store output connections
self._connections = None
- self.node_names = []
def __getattr__(self, ... |
nipype__pydra-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydra/engine/task.py:FunctionTask.__init__",
"pydra/engine/task.py:FunctionTask._run_task"
],
"edited_modules": [
"pydra/engine/task.py:FunctionTask"
]
},
"file... | nipype/pydra | 2b0934e339e3809971a4d966ddbd755ba5c8607e | functions with multiple values in return statement
If default `out` for output is used (without defining `output_names` - will be in pr) and a function returns two values, only one value is saved. See:
```
@pydra.to_task
def add_vector(x1, y1, x2, y2):
return (x1 + x2, y1 + y2)
task5 = add_vector(name="add... | diff --git a/.travis.yml b/.travis.yml
index 715b9cb8..1c6f6392 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,8 +14,6 @@ env:
- CHECK_TYPE="test"
- INSTALL_TYPE="pip"
- INSTALL_DEPENDS="pip setuptools"
- - PIP_ARGS=""
-
matrix:
- INSTALL_TYPE="install"
- INSTALL_TYPE="develop"
@@ -28,... |
nirum__tableprint-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "tableprint/metadata.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tableprint/pr... | nirum/tableprint | 0e658c09c0fd2e77c52b5403e4326093ac5fdff5 | Feature request: Horizontal alignment
This is a simple, lightweight, and awesome package and exactly what I needed to print some database data in my CLI app. Any chance you could add two parameters for horizontal alignment that takes a string for the alignment of the cell data, such as "left", "center", or "right"? S... | diff --git a/Makefile b/Makefile
index 6ad5c19..6fa34eb 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,7 @@ upload:
twine upload dist/*
test2:
- python2 /Users/nirum/anaconda/bin/nosetests --logging-level=INFO
+ python2 -m nose --logging-level=INFO
test:
nosetests -v --with-coverage --cover-package=tableprin... |
nismod__smif-313 | [
{
"changes": {
"added_entities": [
"src/smif/data_layer/data_handle.py:DataHandle.read_coefficients",
"src/smif/data_layer/data_handle.py:DataHandle.write_coefficients"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/smif/data_lay... | nismod/smif | 03e0ab8be750a608c19471d56dd4154fdd402b01 | 'DataHandle' object has no attribute 'read_coefficients'
Adaptors expect data_handle to have method `read_coefficients`. The store has read and write methods for coefficients, but this isn't exposed at the data_handle level.
```python
Traceback (most recent call last):
File "/vagrant/smif/src/smif/controller/sc... | diff --git a/src/smif/data_layer/data_handle.py b/src/smif/data_layer/data_handle.py
index 40401cc8..def4b820 100644
--- a/src/smif/data_layer/data_handle.py
+++ b/src/smif/data_layer/data_handle.py
@@ -555,6 +555,14 @@ class DataHandle(object):
decision_iteration
)
+ def read_coefficients(se... |
nismod__smif-325 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/smif/convert/adaptor.py:Adaptor.get_coefficients"
],
"edited_modules": [
"src/smif/convert/adaptor.py:Adaptor"
]
},
"file": "src/smif/convert/adaptor.py"
},
{
... | nismod/smif | 5e0e04bf7718d1d8a814660f7cbde131760cde2b | Adapter coefficient data should be keyed by the set of dimension names within a spec pair
Coefficients for performing conversions do not need to be generated for every Spec pair, but for every unique Spec dimension pairing. | diff --git a/ci/install.sh b/ci/install.sh
index d6cac22b..2a4d8d29 100755
--- a/ci/install.sh
+++ b/ci/install.sh
@@ -15,20 +15,29 @@ if [[ "$DISTRIB" == "conda" ]]; then
deactivate
# Use the miniconda installer for faster download / install of conda
- # itself
- wget http://repo.continuum.io/minicon... |
nismod__smif-330 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/smif/http_api/register.py:register_routes"
],
"edited_modules": [
"src/smif/http_api/register.py:register_routes"
]
},
"file": "src/smif/http_api/register.py"
}
] | nismod/smif | d0f54ffa3ed5c7458205a20a949520738ab85d20 | smif app throws TemplateNotFound when run from fresh source checkout
The fix is [documented](https://smif.readthedocs.io/en/latest/developers.html#install) - it's missing the template because we need to `npm i; npm run build` - but this exception should be caught and a clearer message shown.
Details:
```
ERROR ... | diff --git a/.appveyor.yml b/.appveyor.yml
index 99bf76e5..7cd7b73c 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -8,16 +8,19 @@ environment:
PGPORT: 5432
PGPASSWORD: Password12!
matrix:
- - PYTHON_VERSION: 3.6
+ - PYTHON_VERSION: 3.7
MINICONDA: C:\Miniconda3-x64
init:
- "ECHO %PYTHON_... |
nismod__smif-379 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/smif/data_layer/store.py:Store.read_scenario_variant_data_multiple_timesteps"
],
"edited_modules": [
"src/smif/data_layer/store.py:Store"
]
},
"file": "src/smif/dat... | nismod/smif | f1350087dc1cc76555be27a6eb1ae37dc5092b17 | results - Results.read_scenario_data reads in incorrect data
results.read_scenario_data reads in the wrong data, and the data changes as the list of timesteps passed changes. Somewhere, there is a misalignment between the Spec coordinates and the data.
For example, actual data:
timestep | lad_uk_2016 | residenti... | diff --git a/src/smif/data_layer/store.py b/src/smif/data_layer/store.py
index 81dfd898..5ae27a54 100644
--- a/src/smif/data_layer/store.py
+++ b/src/smif/data_layer/store.py
@@ -23,6 +23,7 @@ from operator import itemgetter
from typing import Dict, List, Optional
import numpy as np # type: ignore
+
from smif.dat... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.