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Master work flow #2429

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merged 10 commits into from
Feb 10, 2025
Merged

Master work flow #2429

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f054ee5
Deploying to master from @ opencobra/cobratoolbox@4a45a0782f96d31bc3d…
rmtfleming Feb 6, 2025
9e5b119
deploy: 4a45a0782f96d31bc3d56cc3e6a1d326e6376ccb
rmtfleming Feb 6, 2025
73f4f0f
deploy: 4a45a0782f96d31bc3d56cc3e6a1d326e6376ccb
rmtfleming Feb 6, 2025
0216fec
deploy: 73f4f0fdc92d0afb439202fda01915ea697579e1
farid-zare Feb 6, 2025
a224cd6
deploy: 0216fec8cdaa5e7d794ac747395542c266dd5ddd
MetNetComp Feb 10, 2025
96a9e06
Update UpdateContributors.yml
farid-zare Feb 10, 2025
de20865
Update UpdateFunctionDocs.yml
farid-zare Feb 10, 2025
3710bb9
Update UpdateTutorialIndex.yml
farid-zare Feb 10, 2025
22fbc71
Update UpdateFunctionDocs.yml
farid-zare Feb 10, 2025
98ecbd5
Update UpdateContributors.yml
farid-zare Feb 10, 2025
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65 changes: 35 additions & 30 deletions .github/workflows/UpdateContributors.yml
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@@ -1,38 +1,43 @@
name: Update Contributors list

on:
pull_request_target:
types:
- closed
branches: [ master ]

push:
branches:
- develop

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: '3.10'
- name: Install dependencies
working-directory: ./documentation/source/Contributions
run: |
pip install -r requirements.txt
- name: Update contributors
working-directory: ./documentation/source/Contributions
run: |
python UpdateContributorsList.py
- name: generate HTML file
working-directory: ./documentation/source/Contributions
run: |
python GenerateContributorsHTML.py
- name: Deploy to docs
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/source/Contributions/contributors
publish_branch: master
keep_files: true
destination_dir: docs
- uses: actions/checkout@v3

- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: '3.10'

- name: Install dependencies
working-directory: ./documentation/source/Contributions
run: |
pip install -r requirements.txt

- name: Update contributors
working-directory: ./documentation/source/Contributions
run: |
python UpdateContributorsList.py

- name: Generate HTML file
working-directory: ./documentation/source/Contributions
run: |
python GenerateContributorsHTML.py

- name: Deploy to docs
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/source/Contributions/contributors
publish_branch: develop
keep_files: true
destination_dir: docs
commit_message: "Update Contributors (Automatic Workflow)"
120 changes: 66 additions & 54 deletions .github/workflows/UpdateFunctionDocs.yml
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Original file line number Diff line number Diff line change
@@ -1,63 +1,75 @@
name: Update function docs

on:
pull_request_target:
types:
- closed
branches: [ master ]
push:
branches:
- develop

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: '3.10'
- name: Install dependencies
working-directory: ./documentation
run: |
pip install -r requirements.txt
- name: Generate publications rst file
working-directory: ./documentation/source/sphinxext
run: |
python GenerateCitationsRST.py
- name: Update packages
working-directory: ./documentation/source
run: |
python ./sphinxext/copy_files.py
- name: Generate functions rst files
working-directory: ./documentation/source/modules
run: |
python ./GetRSTfiles.py
- name: generate documentation
working-directory: ./documentation
run: |
make html
- name: Copy the citations html page
run: |
cp ./documentation/build/html/citations.html ./documentation/source/Citations/citations.html
- name: Deploy the function modules
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: ./documentation/build/html/modules
branch: master
target-folder: docs/modules
- name: Deploy the citations page
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/source/Citations
publish_branch: master
keep_files: true
destination_dir: docs
- name: Deploy the citations static page
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/build/html/_static
publish_branch: master
keep_files: true
destination_dir: docs/_static
- uses: actions/checkout@v3

- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
python-version: '3.10'

- name: Install dependencies
working-directory: ./documentation
run: |
pip install -r requirements.txt

- name: Generate publications rst file
working-directory: ./documentation/source/sphinxext
run: |
python GenerateCitationsRST.py

- name: Update packages
working-directory: ./documentation/source
run: |
python ./sphinxext/copy_files.py

- name: Generate functions rst files
working-directory: ./documentation/source/modules
run: |
python ./GetRSTfiles.py

- name: Generate documentation
working-directory: ./documentation
run: |
make html

- name: Copy the citations html page
run: |
cp ./documentation/build/html/citations.html ./documentation/source/Citations/citations.html

- name: Deploy the function modules
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: ./documentation/build/html/modules
branch: develop
target-folder: docs/modules
commit-message: "update Function Docs (Automatic Workflow)"

- name: Deploy the citations page
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/source/Citations
publish_branch: develop
keep_files: true
destination_dir: docs
commit_message: "update Function Docs (Automatic Workflow)"

- name: Deploy the citations static page
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/build/html/_static
publish_branch: develop
keep_files: true
destination_dir: docs/_static
commit_message: "update Function Docs (Automatic Workflow)"
4 changes: 2 additions & 2 deletions .github/workflows/UpdateTutorialIndex.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: Extract HTML Info

on:
push:
branches: [master]
branches: [develop]
paths:
- '**.html'

Expand Down Expand Up @@ -54,5 +54,5 @@ jobs:
git config user.name "github-actions[bot]"
git config user.email "github-actions[bot]@users.noreply.github.com"
git add .
git commit -m "Sync files from source repo" || echo "No changes to commit"
git commit -m "Update Tutorial (Automatic Workflow)" || echo "No changes to commit"
git push origin master
2 changes: 1 addition & 1 deletion docs/_static/json/functions.json
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66 changes: 33 additions & 33 deletions docs/_static/pygments.css
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Original file line number Diff line number Diff line change
Expand Up @@ -6,70 +6,70 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
.highlight .hll { background-color: #ffffcc }
.highlight { background: #eeffcc; }
.highlight .c { color: #408090; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .err { border: 1px solid #F00 } /* Error */
.highlight .k { color: #007020; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .o { color: #666 } /* Operator */
.highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #007020 } /* Comment.Preproc */
.highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gr { color: #F00 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #333333 } /* Generic.Output */
.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
.highlight .go { color: #333 } /* Generic.Output */
.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .gt { color: #04D } /* Generic.Traceback */
.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #007020 } /* Keyword.Pseudo */
.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #902000 } /* Keyword.Type */
.highlight .m { color: #208050 } /* Literal.Number */
.highlight .s { color: #4070a0 } /* Literal.String */
.highlight .na { color: #4070a0 } /* Name.Attribute */
.highlight .s { color: #4070A0 } /* Literal.String */
.highlight .na { color: #4070A0 } /* Name.Attribute */
.highlight .nb { color: #007020 } /* Name.Builtin */
.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
.highlight .no { color: #60add5 } /* Name.Constant */
.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
.highlight .nc { color: #0E84B5; font-weight: bold } /* Name.Class */
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.highlight .ni { color: #D55537; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #007020 } /* Name.Exception */
.highlight .nf { color: #06287e } /* Name.Function */
.highlight .nf { color: #06287E } /* Name.Function */
.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
.highlight .nn { color: #0E84B5; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #bb60d5 } /* Name.Variable */
.highlight .nv { color: #BB60D5 } /* Name.Variable */
.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .w { color: #BBB } /* Text.Whitespace */
.highlight .mb { color: #208050 } /* Literal.Number.Bin */
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.highlight .mh { color: #208050 } /* Literal.Number.Hex */
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