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89,741 | 31.03.2017 09:08:28 | -7,200 | 85f64865dee362fdf8cb367dd3b947c5a3e4842e | doc: clean up docs and integrate README.rst and CONTRIBUTING.rst | [
{
"change_type": "MODIFY",
"old_path": "docs/cobrapy_difference.rst",
"new_path": "docs/cobrapy_difference.rst",
"diff": "@@ -47,4 +47,4 @@ cobrapy:\n# proceed\nIt is important to note that cameo models maintain `optimize` to maintain\n-compatibility with cobrapy but we discourage its use.\n+compati... | Python | Apache License 2.0 | biosustain/cameo | doc: clean up docs and integrate README.rst and CONTRIBUTING.rst |
89,741 | 31.03.2017 15:05:17 | -7,200 | ad8aa45bd5331147916fcc745cd4200a3821793e | fix: deploy docs even if it is not a tagged commit | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -38,7 +38,7 @@ before_install:\n- 'echo \"this is a build for: $TRAVIS_BRANCH\"'\n- 'if [[ \"$TRAVIS_BRANCH\" != \"devel\" ]]; then bash ./.travis/install_cplex.sh; fi'\ninstall:\n-- pip install flake8 numpy... | Python | Apache License 2.0 | biosustain/cameo | fix: deploy docs even if it is not a tagged commit (#150) |
89,741 | 31.03.2017 18:35:36 | -7,200 | f5d489b991fe1874b472e78a2d17c4a7bd36c8aa | fix: return to build dir on travis after building docs | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -47,6 +47,7 @@ script:\nafter_success:\n- codecov\n- if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then cd docs && make html && echo \"cameo.bio\" > _build/html/CNAME; fi\n+ - cd $TRAVIS_BUILD_DIR\nnotificatio... | Python | Apache License 2.0 | biosustain/cameo | fix: return to build dir on travis after building docs |
89,741 | 31.03.2017 19:15:36 | -7,200 | 9d1705f6121c139e78ceb9bb284e7bdd37347d33 | fix: diagnose problem with gh-pages deployment | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -73,7 +73,7 @@ deploy:\nrepo: biosustain/cameo\ndocs_dir: docs/_build/html\n- provider: pages\n- local_dir: docs/_build/html\n+ local_dir: docs\nskip_cleanup: true\ngithub_token: $GH_TOKEN # Set in travis-ci... | Python | Apache License 2.0 | biosustain/cameo | fix: diagnose problem with gh-pages deployment |
89,741 | 31.03.2017 19:26:44 | -7,200 | 6f9887764aef7b37f391dbc8e7fbc330732b4ace | fix: build docs right before deployment | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -46,8 +46,6 @@ script:\n- pytest -v -rsx --cov --cov-report=xml\nafter_success:\n- codecov\n- - if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then cd docs && make html && echo \"cameo.bio\" > _build/html/CNAME... | Python | Apache License 2.0 | biosustain/cameo | fix: build docs right before deployment |
89,741 | 31.03.2017 19:29:38 | -7,200 | bcaa1b4eecd18145e275bebf3dbb9abdc158b7b1 | fix: install sphinx to fix deployment | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -39,7 +39,7 @@ before_install:\n- 'if [[ \"$TRAVIS_BRANCH\" != \"devel\" ]]; then bash ./.travis/install_cplex.sh; fi'\ninstall:\n- pip install flake8 numpy scipy pyzmq pandas pytest pytest-cov\n-- pip insta... | Python | Apache License 2.0 | biosustain/cameo | fix: install sphinx to fix deployment |
89,741 | 31.03.2017 19:42:48 | -7,200 | 7a67a2b7e77d52b52693f7070ba1708a78bb85cf | chore: set CNAME via provider | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -39,7 +39,7 @@ before_install:\n- 'if [[ \"$TRAVIS_BRANCH\" != \"devel\" ]]; then bash ./.travis/install_cplex.sh; fi'\ninstall:\n- pip install flake8 numpy scipy pyzmq pandas pytest pytest-cov\n-- pip insta... | Python | Apache License 2.0 | biosustain/cameo | chore: set CNAME via provider |
89,741 | 31.03.2017 20:01:23 | -7,200 | 387524e3b50cead585b6cee52f99d517f7a4d7d7 | fix: create .nojekyll file in docs | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -55,7 +55,7 @@ notifications:\nbefore_deploy:\n- pip install twine\n- python setup.py sdist bdist_wheel\n- - if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then cd docs && make html; fi\n+ - if [[ $TRAVIS_PYTHO... | Python | Apache License 2.0 | biosustain/cameo | fix: create .nojekyll file in docs |
89,737 | 03.04.2017 11:20:05 | -7,200 | 6ac3a268b382c3df15469da7db0a9a58fd9b63cb | feat: add a time limit to heuristic optimization
Also added fix documentation and unit tests. | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -74,9 +74,11 @@ class _OptimizationRunner(object):\nclass _OptGeneRunner(_OptimizationRunner):\ndef __call__(self, strategy):\nmax_evaluations = 15000\n+ max_time = (45, 0)\nif self.debug... | Python | Apache License 2.0 | biosustain/cameo | feat: add a time limit to heuristic optimization
Also added fix documentation and unit tests. |
89,733 | 11.04.2017 15:14:30 | -7,200 | db8da3430741ec0fa6b5fdd719429c2766a4ad35 | fix: remove duplicated target entries
And unit tests. | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/heuristic/evolutionary/optimization.py",
"new_path": "cameo/strain_design/heuristic/evolutionary/optimization.py",
"diff": "@@ -625,9 +625,9 @@ class TargetOptimizationResult(Result):\nfor index, solution in enumerate(solutions):\ntargets =... | Python | Apache License 2.0 | biosustain/cameo | fix: remove duplicated target entries (#155)
And unit tests. |
89,737 | 24.05.2017 14:56:02 | -7,200 | 1cfa12ff020cce0cc914a5e49d63b581a60e65d9 | add make api | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -55,7 +55,7 @@ notifications:\nbefore_deploy:\n- pip install twine\n- python setup.py sdist bdist_wheel\n- - if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then cd docs && make html && touch _build/html/.nojeky... | Python | Apache License 2.0 | biosustain/cameo | add make api |
89,734 | 29.05.2017 13:09:21 | -7,200 | 6d409284d407ea60054e1d8d97ec1ed27f89e905 | feat: move travis testing to being tox based | [
{
"change_type": "ADD",
"old_path": null,
"new_path": ".tox_install.sh",
"diff": "+#!/usr/bin/env bash\n+\n+pip \"$@\"\n+\n+# On Travis CI quickly install python-libsbml wheels.\n+if [[ -n \"${CI}\" && \"${TOXENV}\" != \"flake8\" ]]; then\n+ pip install --find-links https://s3.eu-central-1.amazonaws... | Python | Apache License 2.0 | biosustain/cameo | feat: move travis testing to being tox based |
89,741 | 06.06.2017 16:46:27 | -7,200 | aaa2e3c9f621563232fadccdf678b1822071cb25 | fix: add blank line after markup to avoid rst warning
Thank you for spotting this. | [
{
"change_type": "MODIFY",
"old_path": "README.rst",
"new_path": "README.rst",
"diff": "@@ -56,6 +56,7 @@ provide examples and tutorials and also form part of the documentation. They are\nFurthermore, course materials for a two day cell factory engineering course are available `here <https://biosust... | Python | Apache License 2.0 | biosustain/cameo | fix: add blank line after markup to avoid rst warning (#171)
Thank you for spotting this. |
89,735 | 20.03.2017 12:49:08 | -3,600 | 8e0ae78b0b5664d83c283432e1449c06c5715410 | refactor: remove gene/metabolite id
Moved to cobra.core | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/gene.py",
"new_path": "cameo/core/gene.py",
"diff": "@@ -41,25 +41,25 @@ class Gene(cobra.core.Gene):\nif model is not None:\nnew_gene._model = model\nreturn new_gene\n-\n- @property\n- def id(self):\n- return getattr(self, \"_id\", None) # Returns ... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove gene/metabolite id
Moved to cobra.core |
89,735 | 20.03.2017 13:28:12 | -3,600 | 32d28531add11a31b1223d9404159f4dcd9d34ec | refactor: remove reaction bound setters
Moved cobra.core.Reaction | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -106,203 +106,204 @@ class Reaction(_cobrapy.core.Reaction):\nname : str, optional\nThe name of the reaction.\n\"\"\"\n- super(Reaction, self).__init__(id=id, name=name, subsystem=subsy... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction bound setters
Moved cobra.core.Reaction |
89,735 | 20.03.2017 18:09:23 | -3,600 | ab2afce9a245f960646947a0c8447dc7d745e0a6 | refactor: replace model.solve() w model.optimize()
cobra.core.Model.optimize has been improved, removing the need for
model.solve. | [
{
"change_type": "MODIFY",
"old_path": "cameo/__init__.py",
"new_path": "cameo/__init__.py",
"diff": "@@ -29,8 +29,8 @@ from cameo import load_model\n# load a model from SBML format (can be found under cameo/tests/data)\nmodel = load_model('EcoliCore.xml')\n-# solve the model and print the objective... | Python | Apache License 2.0 | biosustain/cameo | refactor: replace model.solve() w model.optimize()
cobra.core.Model.optimize has been improved, removing the need for
model.solve. |
89,735 | 20.03.2017 18:09:56 | -3,600 | 34ee2dbc3c201ad439d41b5b8e41da20e0915baf | refactor: remove model.S
Avoid capital letter attributes and use the cobra implementation of the
S matrix. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -632,18 +632,18 @@ class SolverBasedModel(cobra.core.Model):\nreturn essential\n- @property\n- def S(self):\n- metabolite_index = {metabolite.id: index for index, me... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove model.S
Avoid capital letter attributes and use the cobra implementation of the
S matrix. |
89,735 | 21.03.2017 09:00:23 | -3,600 | a96d72443d57c8869ae62ab29640cc6a3279354b | refactor: remove fix_objective_as_constraint
Replace with the cobrapy implementation (which is pretty much identical) | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -372,37 +372,37 @@ class SolverBasedModel(cobra.core.Model):\nself.add_reactions([reaction])\nreturn reaction\n- def fix_objective_as_constraint(self, time_machine=N... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove fix_objective_as_constraint
Replace with the cobrapy implementation (which is pretty much identical) |
89,735 | 21.03.2017 16:50:04 | -3,600 | 27361401619a33c2285fa4025dc95dd6ebe4666e | refactor: remove non_functional_genes
This method was unused/tested. Remove in favor of new implementation
elsewhere. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -21,11 +21,9 @@ from __future__ import absolute_import, print_function\nimport csv\nimport logging\n-from copy import copy, deepcopy\nfrom functools import partial\n... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove non_functional_genes
This method was unused/tested. Remove in favor of new implementation
elsewhere. |
89,735 | 22.03.2017 14:37:37 | -3,600 | ef1310ae3977f695ad6e0d7fee3e35d833df488b | refactor: move add_exchange and _reaction_for
Move these functions out of SolverBasedModel and refactor them to use
new cobrapy functionality. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/metabolite.py",
"new_path": "cameo/core/metabolite.py",
"diff": "@@ -17,6 +17,7 @@ from functools import partial\nimport cobra\nimport six\nfrom cameo.util import inheritdocstring\n+from cameo.core.utils import add_exchange\nlogger = logging.getLogg... | Python | Apache License 2.0 | biosustain/cameo | refactor: move add_exchange and _reaction_for
Move these functions out of SolverBasedModel and refactor them to use
new cobrapy functionality. |
89,735 | 22.03.2017 14:54:27 | -3,600 | 927e03ff624bf32ea0676e765b0498c30800671a | refactor: remove add_ratio_constraint
This method is not actually used anywhere in cameo and is somewhat
convoluted. Remove completely in favor of directly formulating
constraints and adding them as only marginally more effort but
considerably more explicit. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -26,11 +26,9 @@ from functools import partial\nimport cobra\nimport optlang\nimport six\n-import sympy\nfrom pandas import DataFrame, pandas\nfrom sympy import Add\n... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove add_ratio_constraint
This method is not actually used anywhere in cameo and is somewhat
convoluted. Remove completely in favor of directly formulating
constraints and adding them as only marginally more effort but
considerably more explicit. |
89,735 | 22.03.2017 15:28:44 | -3,600 | 6c180f1b49652c2a5b02a786f604731e6dfa44ca | refactor: move essential_{genes, reactions, meta}
Simply move these out of the SolverBasedModel class in a step towards
removing this class altogether. These functions could possibly be
further moved to cobrapy altogether. | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/deterministic/linear_programming.py",
"new_path": "cameo/strain_design/deterministic/linear_programming.py",
"diff": "@@ -33,7 +33,7 @@ from cameo.core.strain_design import StrainDesignMethodResult, StrainDesignMetho\nfrom cameo.core.target... | Python | Apache License 2.0 | biosustain/cameo | refactor: move essential_{genes, reactions, meta}
Simply move these out of the SolverBasedModel class in a step towards
removing this class altogether. These functions could possibly be
further moved to cobrapy altogether. |
89,735 | 23.03.2017 10:54:42 | -3,600 | f7821d7348326175010778c6df81e613aab01b7b | refactor: remove model._ids_to_reactions
Replaced with `DictList.get_by_any` which does pretty much the same
thing. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -499,11 +499,11 @@ class SolverBasedModel(cobra.core.Model):\n# else:\n# return solution\n- def __dir__(self):\n- # Hide 'optimize' from user.\n- fields = sorted(dir... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove model._ids_to_reactions
Replaced with `DictList.get_by_any` which does pretty much the same
thing. |
89,735 | 23.03.2017 12:03:47 | -3,600 | 70be2c50e622ab25e59bdd7fb0cad325f71eb04b | refactor: remove model.change_objective
Replaced with model.objective setter which now has context support. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "@@ -21,7 +21,6 @@ from __future__ import absolute_import, print_function\nimport csv\nimport logging\n-from functools import partial\nimport cobra\nimport optlang\n@@ -... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove model.change_objective
Replaced with model.objective setter which now has context support. |
89,735 | 23.03.2017 16:17:45 | -3,600 | f25951e055b9bca77dcda74921f35f6767c9f9cc | refactor: remove reaction.add_metabolites
Not needed anymore | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -18,7 +18,7 @@ from __future__ import absolute_import, print_function\nimport logging\nfrom functools import partial\n-import cobra as _cobrapy\n+import cobra\nimport six\nimport cameo\... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction.add_metabolites
Not needed anymore |
89,735 | 24.03.2017 17:50:15 | -3,600 | 1fcf3c6cd2969034cb1e4e7016c43a3d59e20102 | refactor: move metabolite.knock_out add_exchange
Move these to cobra. metabolite.knock_out must be metabolite method to
enable target.knock_out symmetry. Depends on add_exchange | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/metabolite.py",
"new_path": "cameo/core/metabolite.py",
"diff": "# See the License for the specific language governing permissions and\n# limitations under the License.\nimport logging\n-from functools import partial\nimport cobra\nimport six\nfrom ... | Python | Apache License 2.0 | biosustain/cameo | refactor: move metabolite.knock_out add_exchange
Move these to cobra. metabolite.knock_out must be metabolite method to
enable target.knock_out symmetry. Depends on add_exchange |
89,735 | 24.03.2017 18:01:37 | -3,600 | 33ca70a657e5fc54b1391193aa7d7ae656baea86 | refactor: remove reaction.change_bounds
obsolete with reaction.bounds | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -332,9 +332,9 @@ class Designer(object):\nif isinstance(host, Model):\nhost = Host(name='UNKNOWN_HOST', models=[host])\nfor model in list(host.models):\n- with TimeMachine() as tm:\n+ wit... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction.change_bounds
obsolete with reaction.bounds |
89,735 | 24.03.2017 18:03:00 | -3,600 | 8118b56bd6034a82392dfa1cd67bf58c03d3ab45 | refactor: remove reaction.{flux, reduced_costs}
in favor of the identical properties from super | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -349,19 +349,19 @@ class Reaction(cobra.core.Reaction):\nremove_cycles=False)\nreturn fva_result['upper_bound'][self.id]\n- @property\n- def flux(self):\n- if self.model is not None:\n-... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction.{flux, reduced_costs}
in favor of the identical properties from super |
89,735 | 24.03.2017 18:04:34 | -3,600 | 248e72ebd5761e5773ec75b128996b62f43946de | refactor: remove reaction.effective_bounds
Cobrapy's model.summary does something very similar, use that instead. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -335,19 +335,19 @@ class Reaction(cobra.core.Reaction):\n# model.objective += coef_difference * self.flux_expression\n# self._objective_coefficient = value\n- @property\n- def effective... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction.effective_bounds
Cobrapy's model.summary does something very similar, use that instead. |
89,735 | 24.03.2017 18:07:35 | -3,600 | 18254adfa65183a81fc9c548fd7d3ebf66cd9d46 | refactor: remove reaction.pop
unused | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -21,8 +21,6 @@ import cobra\nimport six\nimport cameo\n-from cameo import flux_analysis\n-from cameo.parallel import SequentialView\nfrom cameo.util import inheritdocstring\nlogger = lo... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove reaction.pop
unused |
89,735 | 24.03.2017 18:11:40 | -3,600 | d630a3cbf6f58cb4ddb1132c4e1247570db6f9b8 | refactor: remove redundant reaction.is_exchange
super has boundary which is equivalent | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -361,9 +361,9 @@ class Reaction(cobra.core.Reaction):\n# else:\n# return None\n- @property\n- def is_exchange(self):\n- return (len(self.reactants) == 0 or len(self.products) == 0) and ... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove redundant reaction.is_exchange
super has boundary which is equivalent |
89,735 | 27.03.2017 09:26:11 | -7,200 | fe66e621950ad0cb9aabe48f3f9a7666e5a614e2 | refactor: remove n_carbon
Newly introduced but hardly used attribute for metabolite and
reaction. Remove it in favor of considering more general property. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/metabolite.py",
"new_path": "cameo/core/metabolite.py",
"diff": "# Copyright 2016 Novo Nordisk Foundation Center for Biosustainability, DTU.\n-\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except ... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove n_carbon
Newly introduced but hardly used attribute for metabolite and
reaction. Remove it in favor of considering more general property. |
89,735 | 27.03.2017 09:54:07 | -7,200 | 0a402205be303cdc9bd43a977576a029997e7195 | refactor: move medium definitions
In favor of cobrapy's medium definition. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solver_based_model.py",
"new_path": "cameo/core/solver_based_model.py",
"diff": "from __future__ import absolute_import, print_function\n-import csv\nimport logging\nimport cobra\nimport optlang\nimport six\n-from pandas import DataFrame, pandas\nfr... | Python | Apache License 2.0 | biosustain/cameo | refactor: move medium definitions
In favor of cobrapy's medium definition. |
89,735 | 27.03.2017 10:14:46 | -7,200 | a4c814d394f4f2f459c9707a4fb53afa930a1936 | refactor: remove solution classes
merged and improved upstream, no need to subclass | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/solution.py",
"new_path": "cameo/core/solution.py",
"diff": "# See the License for the specific language governing permissions and\n# limitations under the License.\n-from __future__ import absolute_import, print_function\n-\n-import datetime\n-impo... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove solution classes
merged and improved upstream, no need to subclass |
89,735 | 27.03.2017 10:24:17 | -7,200 | 84b775c9f027dbfd38f6f8b4d2e61f423291d0ed | refactor: move _repr_html_
move these upstream | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/reaction.py",
"new_path": "cameo/core/reaction.py",
"diff": "@@ -468,27 +468,27 @@ class Reaction(cobra.core.Reaction):\n# number of carbons for all metabolites involved in a reaction\n# \"\"\"\n# return sum(metabolite.n_carbon for metabolite in sel... | Python | Apache License 2.0 | biosustain/cameo | refactor: move _repr_html_
move these upstream |
89,735 | 27.03.2017 12:56:15 | -7,200 | 09b7f9aa713b15a0de79df012a5296f8f7e9561b | refactor: favour model context over time-machine
Where straight-forward, replace the use of TimeMachine with model as
context. | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -46,7 +46,6 @@ from cameo.exceptions import SolveError\nfrom cameo.strain_design import OptGene, DifferentialFVA\nfrom cameo.ui import notice, searching, stop_loader\nfrom cameo.strain_de... | Python | Apache License 2.0 | biosustain/cameo | refactor: favour model context over time-machine
Where straight-forward, replace the use of TimeMachine with model as
context. |
89,735 | 29.03.2017 14:59:21 | -7,200 | 0b8e2a77874b0ede25e1000d55e75a9b18f26233 | refactor: use optlang constants
check status against optlang constants | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -29,7 +29,7 @@ from cobra.util import fix_objective_as_constraint\nfrom numpy import trapz\nfrom six.moves import zip\nfrom sympy import S\n-from optlang.interface imp... | Python | Apache License 2.0 | biosustain/cameo | refactor: use optlang constants
check status against optlang constants |
89,735 | 29.03.2017 15:00:04 | -7,200 | 337c829a9f053b24fb29091e113580883fd55223 | fix: swap_cofactors
Fix remnant use of reaction.swap_cofactors (old bug) | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/heuristic/evolutionary/processing.py",
"new_path": "cameo/strain_design/heuristic/evolutionary/processing.py",
"diff": "# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language ... | Python | Apache License 2.0 | biosustain/cameo | fix: swap_cofactors
Fix remnant use of reaction.swap_cofactors (old bug) |
89,735 | 29.03.2017 16:22:10 | -7,200 | fe9797ad4b3ff722afe6c170ccddab5a433439e6 | refactor: move solver exceptions to cobra
These exceptions are necessary in cobra as well, so let's define them
there and cobra's `assert_optimal` to handle which error to throw. | [
{
"change_type": "MODIFY",
"old_path": "cameo/exceptions.py",
"new_path": "cameo/exceptions.py",
"diff": "@@ -27,24 +27,3 @@ class IncompatibleTargets(Exception):\nclass SolveError(Exception):\ndef __init__(self, message):\nsuper(SolveError, self).__init__(message)\n-\n-\n-class Infeasible(SolveErro... | Python | Apache License 2.0 | biosustain/cameo | refactor: move solver exceptions to cobra
These exceptions are necessary in cobra as well, so let's define them
there and cobra's `assert_optimal` to handle which error to throw. |
89,735 | 29.03.2017 17:00:19 | -7,200 | 6a307e3de8da3259f25908951b76f135fa97e761 | fix: re-enable tests for all solvers | [
{
"change_type": "MODIFY",
"old_path": "tests/conftest.py",
"new_path": "tests/conftest.py",
"diff": "@@ -10,7 +10,6 @@ from cameo.config import solvers\ncameo_directory = abspath(join(dirname(abspath(__file__)), \"..\"))\ncameo_location = abspath(join(cameo_directory, \"..\"))\ndata_dir = join(came... | Python | Apache License 2.0 | biosustain/cameo | fix: re-enable tests for all solvers |
89,735 | 29.03.2017 17:19:31 | -7,200 | b7d0efe714c2be1387fc73af426d4d206ea97014 | fix: skip test for essential metabolites
that one needs some work still.. | [
{
"change_type": "MODIFY",
"old_path": "tests/test_solver_based_model.py",
"new_path": "tests/test_solver_based_model.py",
"diff": "@@ -862,19 +862,24 @@ class TestModel:\ncore_model.reactions.Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2.lower_bound = 999999.\nfind_essential_reactions(core... | Python | Apache License 2.0 | biosustain/cameo | fix: skip test for essential metabolites
that one needs some work still.. |
89,735 | 29.03.2017 16:57:10 | -7,200 | b4d2f191a8a83af9197a7440f400967f9f25bd34 | chore: schedule devel06 for ci
and use cameo branch of cobrapy. Also only pull cplex for py27, 34 as
unavailable for higher versions. | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -21,6 +21,7 @@ branches:\n- master\n- devel\n- devel-nonfree\n+ - devel06\n- /^[0-9]+\\.[0-9]+\\.[0-9]+[.0-9ab]*$/\ncache:\n"
},
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"ne... | Python | Apache License 2.0 | biosustain/cameo | chore: schedule devel06 for ci
and use cameo branch of cobrapy. Also only pull cplex for py27, 34 as
unavailable for higher versions. |
89,735 | 30.03.2017 09:16:19 | -7,200 | 2cd69efb57bfbf16c4621e63718a68ecf6792008 | fix: save pickles in protocol 2 / use glpk
To enable reading in old pythons and with missing cplex | [
{
"change_type": "MODIFY",
"old_path": "tests/data/iJO1366.pickle",
"new_path": "tests/data/iJO1366.pickle",
"diff": "Binary files a/tests/data/iJO1366.pickle and b/tests/data/iJO1366.pickle differ\n"
},
{
"change_type": "MODIFY",
"old_path": "tests/data/salmonella.pickle",
"new_path... | Python | Apache License 2.0 | biosustain/cameo | fix: save pickles in protocol 2 / use glpk
To enable reading in old pythons and with missing cplex |
89,735 | 30.03.2017 09:16:39 | -7,200 | 35db1fddac6b1cbb1e42203df95bff4157d21fa7 | fix: catch SolverNotFound error | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -26,6 +26,7 @@ from cobra import DictList\nfrom sympy import Add, Mul, RealNumber\nfrom cobra import Model, Met... | Python | Apache License 2.0 | biosustain/cameo | fix: catch SolverNotFound error |
89,735 | 30.03.2017 10:35:12 | -7,200 | 725e4e2d4df836ef54fe2e777ec80b631ce19c44 | fix: use iteritems instead of items
iteritems also supported with pandas series | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/deterministic/flux_variability_based.py",
"new_path": "cameo/strain_design/deterministic/flux_variability_based.py",
"diff": "@@ -872,7 +872,7 @@ class FSEOF(StrainDesignMethod):\ntarget.lower_bound = level\ntarget.upper_bound = level\nsolu... | Python | Apache License 2.0 | biosustain/cameo | fix: use iteritems instead of items
iteritems also supported with pandas series |
89,735 | 30.03.2017 14:39:18 | -7,200 | e877911290f85f0c5afc9f0d7c24cb4a56d65c6a | fix: reaction.copy fails across models
Reaction.copy in cobrapy needs refactoring. | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -20,6 +20,7 @@ import warnings\nfrom collections import Counter\nfrom functools import partial\nfrom math impor... | Python | Apache License 2.0 | biosustain/cameo | fix: reaction.copy fails across models
Reaction.copy in cobrapy needs refactoring. |
89,735 | 31.03.2017 10:43:36 | -7,200 | 4a2c90f7f823a5a47daeeee5adfc077af8519bea | fix: sloppy=True for objective def fails w cplex | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/simulation.py",
"new_path": "cameo/flux_analysis/simulation.py",
"diff": "@@ -285,8 +285,7 @@ def lmoma(model, reference=None, cache=None, reactions=None, *args, **kwargs):\ndef create_objective(model, variables):\nreturn model.solver.inter... | Python | Apache License 2.0 | biosustain/cameo | fix: sloppy=True for objective def fails w cplex |
89,735 | 31.03.2017 10:44:48 | -7,200 | 98f749d80439d4d8de8208a4a355cf8762b72f1e | fix: pathway tests manipulate the model
Some tests change the model, causing others to fail. Change the scope. | [
{
"change_type": "MODIFY",
"old_path": "tests/test_pathway_predictions.py",
"new_path": "tests/test_pathway_predictions.py",
"diff": "@@ -38,7 +38,7 @@ def pathway_predictor(request, data_directory, universal_model):\nreturn core_model, predictor\n-@pytest.fixture(scope=\"module\")\n+@pytest.fixture... | Python | Apache License 2.0 | biosustain/cameo | fix: pathway tests manipulate the model
Some tests change the model, causing others to fail. Change the scope. |
89,741 | 05.04.2017 10:32:59 | -7,200 | 7cc84417803d6bef08fc726cd451a7777f4cbc48 | fix: make PathwayPredictor work with custom models | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -27,7 +27,7 @@ from cobra import DictList\nfrom sympy import Add, Mul, RealNumber\nfrom cobra import Model, Met... | Python | Apache License 2.0 | biosustain/cameo | fix: make PathwayPredictor work with custom models |
89,741 | 05.04.2017 14:38:01 | -7,200 | ae4c3adbbb9ab1b3fe8be0cc2648cf65a7de5fde | fix: SolveError -> OptimizationError to catch problems during strain design problems | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -42,7 +42,7 @@ from cameo import fba\nfrom cameo import config, util\nfrom cameo.api.hosts import hosts as HOSTS, Host\nfrom cameo.api.products import products\n-from cameo.exceptions imp... | Python | Apache License 2.0 | biosustain/cameo | fix: SolveError -> OptimizationError to catch problems during strain design problems |
89,741 | 05.04.2017 14:47:30 | -7,200 | d6094c8e29b3b0d38d3ab5899a79c87424c9f7c2 | fix: found another SolveError -> OptimizationError | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -447,7 +447,7 @@ class Designer(object):\ntry:\nflux_dist = fba(model, objective=product)\nreturn flux_dist[product.id] / abs(flux_dist[source.id])\n- except SolveError:\n+ except Optimiz... | Python | Apache License 2.0 | biosustain/cameo | fix: found another SolveError -> OptimizationError |
89,735 | 25.04.2017 11:12:52 | -7,200 | 77e03737bb4038d21ae6bfd6cae429821954e597 | fix: match to work with pre-release cobrapy
use the to_frame() method instead of data_frame property of solution
use the model's add_boundary instead of the temporary add_exchange | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/utils.py",
"new_path": "cameo/core/utils.py",
"diff": "import six\nimport csv\n-from cobra.util import add_exchange\nfrom pandas import DataFrame\n@@ -37,7 +36,7 @@ def get_reaction_for(model, value, add=True):\nreactions = model.reactions.query(\"^... | Python | Apache License 2.0 | biosustain/cameo | fix: match to work with pre-release cobrapy
- use the to_frame() method instead of data_frame property of solution
- use the model's add_boundary instead of the temporary add_exchange |
89,735 | 16.05.2017 15:47:24 | -7,200 | f71ac71b16f2b2a68b62b3e7d27f897f5460fe21 | fix: don't used removed (unused) argument delete
The delete argument had no function in remove_reactions in cobra 0.6 and
was therefore removed. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/pathway.py",
"new_path": "cameo/core/pathway.py",
"diff": "@@ -128,7 +128,7 @@ class Pathway(object):\nif tm is not None:\ntm(do=partial(model.add_reactions, self.reactions),\n- undo=partial(model.remove_reactions, self.reactions, delete=False))\n+ ... | Python | Apache License 2.0 | biosustain/cameo | fix: don't used removed (unused) argument delete
The delete argument had no function in remove_reactions in cobra 0.6 and
was therefore removed. |
89,735 | 16.05.2017 15:48:21 | -7,200 | cf76129b9d2830fab7d950f70e3be8efd3d2a5c5 | refactor: improve ModelDB when failed connection
Instead of making a mock list, when failing to connect, just don't make
an index at all and update the status flag to facilitate skipping tests. | [
{
"change_type": "MODIFY",
"old_path": "cameo/models/webmodels.py",
"new_path": "cameo/models/webmodels.py",
"diff": "@@ -173,13 +173,14 @@ class ModelDB(object):\nself._index_key = index_key\nself._get_model_method = get_model_method\nself._index = None\n+ self.status = ''\ndef _index_models(self):... | Python | Apache License 2.0 | biosustain/cameo | refactor: improve ModelDB when failed connection
Instead of making a mock list, when failing to connect, just don't make
an index at all and update the status flag to facilitate skipping tests. |
89,735 | 14.06.2017 13:56:15 | -7,200 | 7dc125b59ac9e27001bf019fc962b4f9905262e0 | fix: adjust phpp to cobrapy model optimization
should use model.solver.optimize and set or not set fluxes depending on
result, rather than fetching all values (no lazysolution anymore) | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -697,11 +697,12 @@ class _PhenotypicPhasePlaneChunkEvaluator(object):\nreturn [self._production_envelope_inner(point) for point in points]\ndef _interval_estimates(sel... | Python | Apache License 2.0 | biosustain/cameo | fix: adjust phpp to cobrapy model optimization
should use model.solver.optimize and set or not set fluxes depending on
result, rather than fetching all values (no lazysolution anymore) |
89,735 | 27.06.2017 15:56:05 | -7,200 | 4ea73c5d21ef0c03675e834a989c7e17911e09a1 | fix: avoid mutables in defaults
and required argument so no default | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -301,7 +301,7 @@ def flux_variability_analysis(model, reactions=None, fraction_of_optimum=0., pfb\nreturn FluxVariabilityResult(solution)\n-def phenotypic_phase_plane(... | Python | Apache License 2.0 | biosustain/cameo | fix: avoid mutables in defaults
and required argument so no default |
89,734 | 18.07.2017 12:04:16 | -7,200 | 7e6845e3d665f1f44d51c28ab8e57a636c0442de | feat: quick fix for Python 2 on Windows
The stdlib gzip module always adds binary mode 'b' to the read flag. This was
causing a `ValueError` on Python 2 under Windows. | [
{
"change_type": "MODIFY",
"old_path": "cameo/data/metanetx.py",
"new_path": "cameo/data/metanetx.py",
"diff": "@@ -26,7 +26,13 @@ import pandas\nimport cameo\n-with gzip.open(os.path.join(cameo._cameo_data_path, 'metanetx.json.gz'), 'rt') as f:\n+if six.PY2:\n+ flag = 'r'\n+else:\n+ flag = 'rt'\n+\... | Python | Apache License 2.0 | biosustain/cameo | feat: quick fix for Python 2 on Windows
The stdlib gzip module always adds binary mode 'b' to the read flag. This was
causing a `ValueError` on Python 2 under Windows. |
89,735 | 14.07.2017 16:35:50 | -7,200 | 9cef65ee840d8038c4fe8c0cb254b0b2811ac213 | refactor: check compartment regex valid
cryptic failures if compartment regex was not valid, raise some sensible
error instead | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/util.py",
"new_path": "cameo/strain_design/pathway_prediction/util.py",
"diff": "# limitations under the License.\nfrom __future__ import absolute_import, print_function\n-\n-__all__ = ['create_adapter_reactions', 'displa... | Python | Apache License 2.0 | biosustain/cameo | refactor: check compartment regex valid
cryptic failures if compartment regex was not valid, raise some sensible
error instead |
89,735 | 17.07.2017 11:06:05 | -7,200 | ce7d0edb5d039420cb65e0298917fd0cec1bb4bf | refactor: avoid printing long reaction
biomass reaction string too long for any axis, auto-shorten to id | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -403,8 +403,10 @@ def _nice_id(reaction):\nif isinstance(reaction, Reaction):\nif hasattr(reaction, 'nice_id'):\nnice_id = reaction.nice_id\n- else:\n+ elif len(reacti... | Python | Apache License 2.0 | biosustain/cameo | refactor: avoid printing long reaction
biomass reaction string too long for any axis, auto-shorten to id |
89,735 | 18.07.2017 13:55:57 | -7,200 | 6b25a201a7c1be1b8f3674491b84c45fd535b44b | fix: respect essential_genes in optgene
`essential_genes` arg expected to be a list of identifiers, fix bug
assuming list of gene objects. | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/heuristic/evolutionary/optimization.py",
"new_path": "cameo/strain_design/heuristic/evolutionary/optimization.py",
"diff": "@@ -771,8 +771,9 @@ class GeneKnockoutOptimization(KnockoutOptimization):\nif use_nullspace_simplification:\nns = nu... | Python | Apache License 2.0 | biosustain/cameo | fix: respect essential_genes in optgene
`essential_genes` arg expected to be a list of identifiers, fix bug
assuming list of gene objects. |
89,735 | 18.07.2017 14:09:16 | -7,200 | e1ade4cbf65ffc60153218fa14c4df44fba850ac | refactor: remove calls to removed add_demand
Replace `add_demand` with `add_boundary`. Also then became necessary to
remove the time machine argument from deprecated `plug_model`. | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/pathway.py",
"new_path": "cameo/core/pathway.py",
"diff": "@@ -109,10 +109,9 @@ class Pathway(object):\nreaction.name + sep +\nreaction.notes.get(\"pathway_note\", \"\") + \"\\n\")\n- def plug_model(self, model, tm=None):\n+ def plug_model(self, mod... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove calls to removed add_demand
Replace `add_demand` with `add_boundary`. Also then became necessary to
remove the time machine argument from deprecated `plug_model`. |
89,735 | 18.07.2017 16:48:42 | -7,200 | 183a1ba5441afc5dcd8e24ccc6c173a16937f9c6 | fix: adjust to new solution object
Fluxes are now default Series so allow them to be as input to room and moma | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/simulation.py",
"new_path": "cameo/flux_analysis/simulation.py",
"diff": "@@ -81,7 +81,7 @@ def fba(model, objective=None, reactions=None, *args, **kwargs):\nassert_optimal(model)\nsolution = get_solution(model)\nif reactions is not None:\n... | Python | Apache License 2.0 | biosustain/cameo | fix: adjust to new solution object
Fluxes are now default Series so allow them to be as input to room and moma |
89,735 | 19.07.2017 09:08:39 | -7,200 | 105381c6c2c7601f5ea1f5a1b576f9b90d6f2469 | refactor: remove debug print statements | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/deterministic/linear_programming.py",
"new_path": "cameo/strain_design/deterministic/linear_programming.py",
"diff": "@@ -115,14 +115,12 @@ class OptKnock(StrainDesignMethod):\nself._build_problem(exclude_reactions, use_nullspace_simplifica... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove debug print statements |
89,735 | 19.07.2017 12:24:19 | -7,200 | cf0c9ec209cf478219db12e5b01fa5aad0fab5c3 | refactor: simplify optimization with error
Use new feature in cobrapy to raise error if model is infeasible. Avoid
utility imports from cobrapy. | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -27,7 +27,7 @@ import pandas\nimport six\nfrom cobra import Reaction, Metabolite\nfrom cobra.core import get_solution\n-from cobra.util import fix_objective_as_constra... | Python | Apache License 2.0 | biosustain/cameo | refactor: simplify optimization with error
Use new feature in cobrapy to raise error if model is infeasible. Avoid
utility imports from cobrapy. |
89,735 | 19.07.2017 12:25:09 | -7,200 | e16802dff0aeacccbd16f33b538dc0bff2f87542 | refactor: remove cameo.stuff
Untested code not used in the package or associated notebooks, let's put
this somewhere else. | [
{
"change_type": "DELETE",
"old_path": "cameo/stuff/__init__.py",
"new_path": null,
"diff": "-# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.\n-#\n-# Licensed under the Apache License, Version 2.0 (the \"License\");\n-# you may not use this file except in compliance with ... | Python | Apache License 2.0 | biosustain/cameo | refactor: remove cameo.stuff
Untested code not used in the package or associated notebooks, let's put
this somewhere else. |
89,735 | 18.07.2017 14:19:19 | -7,200 | 076d34cfa84683995d26dca9aff042a69ec25900 | refactor: avoid divide by zero
Probably new numpy behavior, instead of raising ZeroDivisionError, a
UserWarning is triggered, adjust to this. | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/structural.py",
"new_path": "cameo/flux_analysis/structural.py",
"diff": "@@ -164,7 +164,7 @@ def find_coupled_reactions_nullspace(model, ns=None, tol=1e-10):\n\"\"\"\nif ns is None:\nns = nullspace(create_stoichiometric_array(model))\n- ma... | Python | Apache License 2.0 | biosustain/cameo | refactor: avoid divide by zero
Probably new numpy behavior, instead of raising ZeroDivisionError, a
UserWarning is triggered, adjust to this. |
89,735 | 19.07.2017 13:25:57 | -7,200 | 2c9bd1d5d5b9c722595be455842f690722e47adc | refactor: replace cameo pfba with cobra pfba
Identical functions except the return value, use cobrapy's pfba and
re-class the return value. | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/simulation.py",
"new_path": "cameo/flux_analysis/simulation.py",
"diff": "@@ -37,7 +37,7 @@ from sympy import Add\nfrom sympy import Mul\nfrom sympy.parsing.sympy_parser import parse_expr\nfrom cobra import Reaction\n-from cobra.flux_analys... | Python | Apache License 2.0 | biosustain/cameo | refactor: replace cameo pfba with cobra pfba
Identical functions except the return value, use cobrapy's pfba and
re-class the return value. |
89,735 | 20.07.2017 13:01:51 | -7,200 | e17b15790427eb8b1367af76d60e65e8d47674ef | refactor: use cobra find_essential_{genes, rxn}
Functions equivalent except that cobra version returns a set and cameo
returned a list | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -155,76 +155,6 @@ def find_essential_metabolites(model, threshold=1e-6, force_steady_state=False):\nreturn essential\n-def find_essential_reactions(model, threshold=1e... | Python | Apache License 2.0 | biosustain/cameo | refactor: use cobra find_essential_{genes, rxn}
Functions equivalent except that cobra version returns a set and cameo
returned a list |
89,735 | 20.07.2017 15:01:38 | -7,200 | 712f552a87d309d5c7ee8e1226e132735b5793ec | refactor: do not use mutables as defaults | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/hosts.py",
"new_path": "cameo/api/hosts.py",
"diff": "@@ -35,7 +35,10 @@ MODEL_DIRECTORY = os.path.join(os.path.join(cameo.__path__[0]), 'models/json')\nclass Host(object):\n- def __init__(self, name='', models=[], biomass=[], carbon_sources=[]):\n+ ... | Python | Apache License 2.0 | biosustain/cameo | refactor: do not use mutables as defaults |
89,735 | 21.07.2017 12:42:05 | -7,200 | 95d5f30d73e02e68ab2b3c430c220864e50c51ce | chore: DRY up requirements
No need to repeat info in setup.py in requirements.txt, following
recommendations in | [
{
"change_type": "MODIFY",
"old_path": "requirements.txt",
"new_path": "requirements.txt",
"diff": "-numpy>=1.9.1\n-scipy>=0.9.0\n-blessings>=1.5.1\n-pandas>=0.18.1\n-ordered-set==1.2\n-inspyred>=1.0\n-cobra>=0.6.0a7\n-optlang>=0.3.0\n-escher>=1.0.0\n-numexpr>=2.4\n-networkx>=1.9.1\n-six>=1.9.0\n-fu... | Python | Apache License 2.0 | biosustain/cameo | chore: DRY up requirements
No need to repeat info in setup.py in requirements.txt, following
recommendations in
https://caremad.io/posts/2013/07/setup-vs-requirement/ |
89,735 | 21.07.2017 14:14:12 | -7,200 | ee6965e2be1abb143abb0644fe5770f15ee431b2 | chore: remove unused plotting_old.py | [
{
"change_type": "DELETE",
"old_path": "cameo/visualization/plotting_old.py",
"new_path": null,
"diff": "-# Copyright 2015 Novo Nordisk Foundation Center for Biosustainability, DTU.\n-\n-# Licensed under the Apache License, Version 2.0 (the \"License\");\n-# you may not use this file except in compl... | Python | Apache License 2.0 | biosustain/cameo | chore: remove unused plotting_old.py |
89,735 | 14.03.2017 10:56:54 | -3,600 | aa9cab02fe8f6e5ce7b64283d57b5deb2990d7b0 | fix: only cplex on 2.7, 3.4
cplex in binary we pull in is only for python 2.7 and 3.4 | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -44,7 +44,7 @@ addons:\nbefore_install:\n- travis_retry pip install --upgrade pip setuptools wheel tox\n- 'echo \"this is a build for: $TRAVIS_BRANCH\"'\n-- 'if [[ \"$TRAVIS_BRANCH\" != \"devel\" ]]; then ba... | Python | Apache License 2.0 | biosustain/cameo | fix: only cplex on 2.7, 3.4 (#133)
cplex in binary we pull in is only for python 2.7 and 3.4 |
89,735 | 28.07.2017 11:15:14 | -7,200 | 62684d6227bbb50b06c053e93b72dc027e3f4fec | docs: add release notes
Let's keep track of what changes between the releases in md files
rather than only github releases. | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "release-notes/0.11.0.md",
"diff": "+# Release notes for cameo 0.11.0\n+\n+## Highlights\n+\n+This a major release with substantial changes to several areas. Cameo pioneered the use of a model class that tightly integrates with the underlying sol... | Python | Apache License 2.0 | biosustain/cameo | docs: add release notes
Let's keep track of what changes between the releases in md files
rather than only github releases. |
89,733 | 01.08.2017 11:33:33 | -7,200 | ff60b56074f8d2f93bcdf4af445362b78681f510 | fix: validate left[i] == right[i] | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/structural.py",
"new_path": "cameo/flux_analysis/structural.py",
"diff": "@@ -191,6 +191,25 @@ def find_coupled_reactions_nullspace(model, ns=None, tol=1e-10):\nreaction_j = non_blocked_reactions[j]\nright = non_blocked_ns[j]\nratio = np.ap... | Python | Apache License 2.0 | biosustain/cameo | fix: validate left[i] == right[i] |
89,737 | 26.08.2017 20:07:25 | -7,200 | 2abe3eb4f169eb85c6fa2eb7b69329919e5d9703 | fix: essential metabolites method breaks with some solvers | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/analysis.py",
"new_path": "cameo/flux_analysis/analysis.py",
"diff": "@@ -94,7 +94,7 @@ def knock_out_metabolite(metabolite, force_steady_state=False):\nreaction_id=\"KO_{}\".format(metabolite.id))\nelse:\nprevious_bounds = metabolite.const... | Python | Apache License 2.0 | biosustain/cameo | fix: essential metabolites method breaks with some solvers |
89,737 | 25.08.2017 11:15:47 | -7,200 | e894bd2638625f43acdda90dfbc228d0e5e3c3df | fix: problem cache refactored to use cobrapy context manager
Updated unit tests
Self validation | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/simulation.py",
"new_path": "cameo/flux_analysis/simulation.py",
"diff": "@@ -24,26 +24,23 @@ Currently implements:\nfrom __future__ import absolute_import, print_function\n+import logging\nimport os\n-import six\n-import pandas\nimport num... | Python | Apache License 2.0 | biosustain/cameo | fix: problem cache refactored to use cobrapy context manager
Updated unit tests
Self validation |
89,737 | 30.08.2017 11:08:43 | -7,200 | 97843f21354fe7e0cc5d996b0db74ad1348218a0 | fix: problem cache reset self-validation improved | [
{
"change_type": "MODIFY",
"old_path": "cameo/util.py",
"new_path": "cameo/util.py",
"diff": "@@ -244,8 +244,8 @@ class ProblemCache(object):\n\"\"\"\nRemoves all constraints and variables from the cache.\n\"\"\"\n- variables = self.variables.keys()\n- constraints = self.constraints.keys()\n+ variab... | Python | Apache License 2.0 | biosustain/cameo | fix: problem cache reset self-validation improved |
89,737 | 31.08.2017 14:09:02 | -7,200 | 4a34ca413277ac98e35683dd01a023e991c1a151 | fix: problem cache reset still doesn't work on a single tests | [
{
"change_type": "MODIFY",
"old_path": "tests/test_flux_analysis.py",
"new_path": "tests/test_flux_analysis.py",
"diff": "@@ -329,6 +329,7 @@ class TestSimulationMethods:\npfba_solution = pfba(core_model)\nessential_reactions = find_essential_reactions(core_model)\ncache = ProblemCache(core_model)\n... | Python | Apache License 2.0 | biosustain/cameo | fix: problem cache reset still doesn't work on a single tests |
89,735 | 31.08.2017 14:48:47 | -7,200 | f6fc50853e852936f78cb7b4062b9410ec30048e | release: 0.11.2 | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "release-notes/0.11.2",
"diff": "+# Release notes for cameo 0.11.2\n+\n+## Fixes\n+\n+- Fix the ProblemCache used in moma, lmoma and room to use cobrapy's\n+ HistoryManager instead of the TimeMachine, resolving an issue which\n+ caused repeated a... | Python | Apache License 2.0 | biosustain/cameo | release: 0.11.2 |
89,736 | 18.10.2017 18:03:39 | -7,200 | 31c80e4b9152c2dbd91ef15a4f6b5fe5e1d6136f | fix: failing to run evolution after pickling | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -132,14 +132,12 @@ class PathwayResult(Pathway, Result, StrainDesign):\nmodel.add_reactions(self.adapters)\nif ... | Python | Apache License 2.0 | biosustain/cameo | fix: failing to run evolution after pickling |
89,741 | 07.11.2017 15:17:30 | -3,600 | 5ef403db97a572a6b283580ae70f1d5967a47457 | doc: docs need jupyter installed because of ipython3 code cell tag | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -59,7 +59,7 @@ before_deploy:\n- pip install twine\n- python setup.py sdist bdist_wheel\n- if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then\n- pip install .[docs];\n+ pip install .[docs,jupyter];\ncd docs &&... | Python | Apache License 2.0 | biosustain/cameo | doc: docs need jupyter installed because of ipython3 code cell tag |
89,733 | 06.02.2018 12:45:48 | -3,600 | 6826ce258412dde3229cc9e6b54db64cab0bef17 | Fix: publication fixes
* fix: update cobra version
* fix: add docstring to the package
To remove any confusion from the reviewers heads. | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/deterministic/linear_programming.py",
"new_path": "cameo/strain_design/deterministic/linear_programming.py",
"diff": "# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language go... | Python | Apache License 2.0 | biosustain/cameo | Fix: publication fixes (#198)
* fix: update cobra version
* fix: add docstring to the package
To remove any confusion from the reviewers heads. |
89,736 | 04.04.2018 15:22:01 | -7,200 | 96d408c6478bd1af282b7a25be61815405c5c868 | hotfix: six string types | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -181,7 +181,7 @@ class Designer(object):\nnotice(\"Starting searching for compound %s\" % product)\ntry:\nproduct = self.__translate_product_to_universal_reactions_model_metabolite(produc... | Python | Apache License 2.0 | biosustain/cameo | hotfix: six string types |
89,741 | 11.04.2018 10:16:17 | -7,200 | 1146ba933f24ba7ed97613d316f135eceb16144f | doc: add citation information to README | [
{
"change_type": "MODIFY",
"old_path": "README.rst",
"new_path": "README.rst",
"diff": "@@ -19,6 +19,8 @@ compute promising strain designs.\nCurious? Head over to `try.cameo.bio <http://try.cameo.bio>`__\nand give it a try.\n+Please cite https://doi.org/10.1021/acssynbio.7b00423 if you've used cameo... | Python | Apache License 2.0 | biosustain/cameo | doc: add citation information to README |
89,736 | 21.06.2018 15:17:15 | -7,200 | 94ce3c1177b85df3edb4065ef0ff4cca0c94d0db | fix: cplex installation | [
{
"change_type": "MODIFY",
"old_path": ".gitignore",
"new_path": ".gitignore",
"diff": "@@ -54,3 +54,6 @@ docs/_build\n/.DS_Store\n.cache\n/coverage.xml\n+\n+cplex/\n+cplex*.tar.gz\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": "... | Python | Apache License 2.0 | biosustain/cameo | fix: cplex installation |
89,736 | 21.06.2018 15:35:01 | -7,200 | cf29bdfdb0eee5b42a8669cbc0115c996c83be0e | fix: cameo for python2.7 | [
{
"change_type": "MODIFY",
"old_path": ".travis/install_cplex.sh",
"new_path": ".travis/install_cplex.sh",
"diff": "set -eu\n# Build on master and tags.\n-# $CPLEX_URL is defined in the Travis repository settings.\n+# $CPLEX_URL and $GH_TOKEN is defined in the Travis repository settings.\nif [[ (\"$... | Python | Apache License 2.0 | biosustain/cameo | fix: cameo for python2.7 |
89,736 | 21.06.2018 15:38:56 | -7,200 | 451690bba787e724f74af2e591703d8c61b60b2e | fix: cameo for python2.7 - reset the variable | [
{
"change_type": "MODIFY",
"old_path": ".travis/install_cplex.sh",
"new_path": ".travis/install_cplex.sh",
"diff": "@@ -12,6 +12,8 @@ if [[ (\"${TRAVIS_BRANCH}\" == \"master\" || -n \"${TRAVIS_TAG}\") \\\nif [ \"${PYTHON_VERSION}\" == \"3.5\" ]\nthen\nPYTHON_VERSION=\"3.4\"\n+ else\n+ PYTHON_VERSION... | Python | Apache License 2.0 | biosustain/cameo | fix: cameo for python2.7 - reset the variable |
89,736 | 21.06.2018 19:38:51 | -7,200 | 5a1e6c2559410fcb07a1714482d2327309acb80e | fix: travis build, skip existing | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -58,6 +58,7 @@ deploy:\nsecure: nxjszXtUzQfnLlfg0cmFjd9gRekXDog6dkkN1rMc7CIWH2gZ1gAX4sNETVChnuSmu9egzhuIkviHstRrdyGoEZ7ZkHlTXmpVAs9AY96eMSejnwHHODhYno0jB7DjGcfejodLF+lo6lWz7S7mXXwML6YLM3xxG+AOjLHlHbPTaKc=\nd... | Python | Apache License 2.0 | biosustain/cameo | fix: travis build, skip existing |
89,734 | 05.11.2018 10:06:27 | -3,600 | 8f65273eb81c4e90987103881d036628f734b7e5 | chore: extend gitignore with PyCharm template | [
{
"change_type": "MODIFY",
"old_path": ".gitignore",
"new_path": ".gitignore",
"diff": "@@ -54,3 +54,109 @@ docs/_build\n/.DS_Store\n.cache\n/coverage.xml\n+### Python template\n+# Byte-compiled / optimized / DLL files\n+__pycache__/\n+*.py[cod]\n+*$py.class\n+\n+# C extensions\n+*.so\n+\n+# Distrib... | Python | Apache License 2.0 | biosustain/cameo | chore: extend gitignore with PyCharm template |
89,734 | 05.11.2018 10:54:19 | -3,600 | 0d08eaab4621dd768226c5ef5f4f23028fe728db | style: conform with flake8 settings | [
{
"change_type": "MODIFY",
"old_path": "cameo/core/pathway.py",
"new_path": "cameo/core/pathway.py",
"diff": "@@ -102,12 +102,14 @@ class Pathway(object):\nwith open(file_path, \"w\") as output_file:\nfor reaction in self.reactions:\nequation = _build_equation(reaction.metabolites)\n- output_file.wr... | Python | Apache License 2.0 | biosustain/cameo | style: conform with flake8 settings |
89,739 | 11.12.2018 03:11:27 | 28,800 | e994d07ef085405927d9635924b05edc9b82528b | Update simulation.py to use solution.objective_value vs. legacy solution.f
* Update simulation.py to use solution.objective_value vs. legacy solution.f
Update simulation.py to use solution.objective_value vs. legacy solution.f
* LNT: Lint lines too long. | [
{
"change_type": "MODIFY",
"old_path": "cameo/flux_analysis/simulation.py",
"new_path": "cameo/flux_analysis/simulation.py",
"diff": "@@ -178,7 +178,8 @@ def moma(model, reference=None, cache=None, reactions=None, *args, **kwargs):\nsolution = model.optimize(raise_error=True)\nif reactions is not No... | Python | Apache License 2.0 | biosustain/cameo | Update simulation.py to use solution.objective_value vs. legacy solution.f (#218)
* Update simulation.py to use solution.objective_value vs. legacy solution.f
Update simulation.py to use solution.objective_value vs. legacy solution.f
* LNT: Lint lines too long. |
89,741 | 12.12.2018 13:10:41 | -3,600 | 20ffb09370c465111428b32c13e936073e65b33d | fix: broken cplex installation on travis-ci | [
{
"change_type": "MODIFY",
"old_path": ".travis/install_cplex.sh",
"new_path": ".travis/install_cplex.sh",
"diff": "set -eu\n# Build on master and tags.\n-# $CPLEX_URL and $GH_TOKEN is defined in the Travis repository settings.\nif [[ (\"${TRAVIS_BRANCH}\" == \"master\" || -n \"${TRAVIS_TAG}\") \\\n... | Python | Apache License 2.0 | biosustain/cameo | fix: broken cplex installation on travis-ci |
89,741 | 06.02.2019 16:16:22 | -3,600 | aa45d592f1b57e0e2629d9eb67ce960fdb9a81af | hotfix: fix integercut ID clash in PathwayPredictor | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -294,9 +294,10 @@ class PathwayPredictor(StrainDesignMethod):\nproduct_reaction = self.model.add_boundary(produ... | Python | Apache License 2.0 | biosustain/cameo | hotfix: fix integercut ID clash in PathwayPredictor |
89,734 | 11.02.2019 12:54:38 | -3,600 | 8489055323c2a22b35625461d9e263d22b8f50fd | style: improve logging statements | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -315,18 +315,19 @@ class PathwayPredictor(StrainDesignMethod):\nif len(vars_to_cut) == 0:\n# no pathway found:\... | Python | Apache License 2.0 | biosustain/cameo | style: improve logging statements |
89,734 | 11.02.2019 13:01:06 | -3,600 | f2f5e7581d79f4cd536934363f21f7cea0f84c40 | refactor: increment integer cut in finally | [
{
"change_type": "MODIFY",
"old_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"new_path": "cameo/strain_design/pathway_prediction/pathway_predictor.py",
"diff": "@@ -371,7 +371,6 @@ class PathwayPredictor(StrainDesignMethod):\npathways.append(pathway)\nlogger.info(\"Max flux:... | Python | Apache License 2.0 | biosustain/cameo | refactor: increment integer cut in finally |
89,734 | 19.06.2019 19:51:42 | -7,200 | 2f4e9107890f031e828701a6c563c0f1626a877f | chore: add missing XML header | [
{
"change_type": "MODIFY",
"old_path": "tests/data/EcoliCore.xml",
"new_path": "tests/data/EcoliCore.xml",
"diff": "+<?xml version='1.0' encoding='utf-8' standalone='no'?>\n<sbml xmlns:fbc=\"http://www.sbml.org/sbml/level3/version1/fbc/version2\" level=\"3\" sboTerm=\"SBO:0000624\" version=\"1\" xml... | Python | Apache License 2.0 | biosustain/cameo | chore: add missing XML header |
89,734 | 19.06.2019 19:52:06 | -7,200 | 9b3f7db636255fc3583078ca9c0d51128ae669ef | chore: update model pickles | [
{
"change_type": "MODIFY",
"old_path": "tests/data/iJO1366.pickle",
"new_path": "tests/data/iJO1366.pickle",
"diff": "Binary files a/tests/data/iJO1366.pickle and b/tests/data/iJO1366.pickle differ\n"
},
{
"change_type": "MODIFY",
"old_path": "tests/data/salmonella.pickle",
"new_path... | Python | Apache License 2.0 | biosustain/cameo | chore: update model pickles |
89,734 | 19.06.2019 20:33:10 | -7,200 | 95802bb8f491fbab4ddedf74ca76591481d90cfc | chore: upload codecov report | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -44,6 +44,9 @@ before_install:\nscript:\n- travis_wait tox\n+after_success:\n+ - bash <(curl -s https://codecov.io/bash)\n+\nbefore_deploy:\n- if [[ $TRAVIS_PYTHON_VERSION == \"3.6\" ]]; then\npip install .[... | Python | Apache License 2.0 | biosustain/cameo | chore: upload codecov report |
89,734 | 20.06.2019 09:41:23 | -7,200 | 2bf6bf80af9ccca81278523a2c5f163859a29869 | chore: update coverage | [
{
"change_type": "DELETE",
"old_path": ".coveragerc",
"new_path": null,
"diff": "-# .coveragerc to control coverage.py\n-[run]\n-branch = True\n-source = cameo\n-omit =\n- cameo/strain_design/heuristic/plotters.py\n- cameo/strain_design/heuristic/multiprocess/plotters.py\n- cameo/visualization/*\n- ... | Python | Apache License 2.0 | biosustain/cameo | chore: update coverage |
89,734 | 21.06.2019 22:20:33 | -7,200 | c20c841960623d9c407c2d9ef484c7c028976b9c | docs: fix some failing docstrings | [
{
"change_type": "MODIFY",
"old_path": "cameo/api/designer.py",
"new_path": "cameo/api/designer.py",
"diff": "@@ -191,8 +191,8 @@ class Designer(object):\n\"\"\"\nOptimize targets for the identified pathways. The optimization will only run if the pathway can be optimized.\n- Arguments\n- ---------\n... | Python | Apache License 2.0 | biosustain/cameo | docs: fix some failing docstrings |
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