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BUGFIX: Typos in GH workflow #54

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merged 41 commits into from
Feb 20, 2024
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e2d35da
Adjustment of flake8 settings
JanNiklasWeder Sep 11, 2022
5a876d6
UPDATE: Repository use Ruff as new linter instead of flake8. Temporal
cambordas Apr 22, 2023
2a96936
First test of test_creation passing from refactor
cambordas Apr 22, 2023
417b86f
Main refactor of creation almost completed
cambordas Apr 24, 2023
e35e9a1
FIX: function create_object now passes to get_reaction the correct model
cambordas May 2, 2023
a445a92
UPDATE: missing UserWarning in create_object for missing genomes for
cambordas May 2, 2023
a82d394
__init__.py includes custom imports
cambordas May 3, 2023
0f7ad41
UPDATED: gene parsing
cambordas Jun 7, 2023
61d9516
NEW: module db_version.py for data versioning
cambordas Jun 27, 2023
ab2e0e0
Test updated to use new data and reflect changes
cambordas Jun 27, 2023
db8f9ac
UPDATE: Message for Super pathways. Not supported
cambordas Aug 23, 2023
85826b7
HOTFIX: missing short summary in pathways
cambordas Aug 23, 2023
6ffb58d
NEW: dependency openpyxl
cambordas Oct 25, 2023
b0ca9d5
NEW: General Docstring updated
cambordas Nov 6, 2023
d111fa2
Merge remote-tracking branch 'origin/fix/lint' into fix/members
cambordas Nov 6, 2023
339f4a8
UPDATE: environment.yml and conf.py for docs
cambordas Nov 6, 2023
fe2aacd
UPDATE: dev environment
cambordas Nov 6, 2023
a76e867
fixed the bug that pandas DataFrame deprecated the append function
LifeWorks Dec 30, 2023
bdca740
Jupyter files updated
cambordas Jan 15, 2024
e47921b
Merge branch 'docs/members' into fix/members
cambordas Jan 15, 2024
616d0bf
Tests update
cambordas Jan 15, 2024
1f3317a
Update: Credentials information in guide
cambordas Jan 15, 2024
870edc2
UPDATED: Escher maps in guides
cambordas Jan 15, 2024
14b93a9
Removal deprecated functions in creation.py
cambordas Jan 16, 2024
e194873
Replacing black with ruff
cambordas Feb 19, 2024
2d29916
Tox now runs the test suite and not GH
cambordas Feb 19, 2024
88bd2d3
Merge remote-tracking branch 'syssynbio/dev' into dev/1.2.0
cambordas Feb 19, 2024
dd65eac
Deprecation warning for Solcyc
cambordas Feb 19, 2024
1f7746f
Refactor of logging for cobramod and visualization
cambordas Feb 19, 2024
d6cbb8a
warning.warn replaced by using logging module
cambordas Feb 19, 2024
d7a0030
Changed behaviour to not open the browser
cambordas Feb 19, 2024
abbb14b
Removing dependency from extra repo
cambordas Feb 19, 2024
66e8157
Removing non-interactive statement
cambordas Feb 19, 2024
a02b4e0
Bump version to 1.2.0
cambordas Feb 19, 2024
5194142
Updated index with current README text
cambordas Feb 20, 2024
8c24c78
Updating text for doc source
cambordas Feb 20, 2024
ffdf0b0
Changelog updated to latest changes
cambordas Feb 20, 2024
f3346be
Missing secret for tests
cambordas Feb 20, 2024
1bbd782
Typo in path for secrets
cambordas Feb 20, 2024
1fe5d23
BUGFIX: typos in workflows
cambordas Feb 20, 2024
dc28c49
Merge branch 'master' into dev/1.2.0
cambordas Feb 20, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/docs-build-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,6 @@ jobs:
conda env update --file environment.yml
- name: Sphinx build
run: |
source activate cobramod
source activate cobramod-dev
conda info
sphinx-build docs/source docs/build
3 changes: 2 additions & 1 deletion .github/workflows/test-build-and-publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -48,10 +48,11 @@ jobs:

steps:
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10
python-version: "3.10"
cache: "pip"

- name: Install dependencies
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