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Develop #2454

Merged
merged 31 commits into from
Mar 11, 2025
Merged

Develop #2454

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8855a07
solver bugs fixed
rmtfleming Nov 7, 2024
85ef00e
test files
rmtfleming Nov 7, 2024
33c8d11
Merge remote-tracking branch 'upstream/develop' into develop
rmtfleming Feb 6, 2025
0227831
Changes to metaboreport and WBM modelling
ithiele Feb 7, 2025
66058ca
update Function Docs (Automatic Workflow)
bramnap Feb 12, 2025
28b6c8a
Merge pull request #2442 from opencobra/master
farid-zare Feb 17, 2025
e7abf4b
Merge branch 'develop' into it_04_07_2024
farid-zare Feb 18, 2025
749fa17
Update testAllCI_step2.yml
farid-zare Feb 18, 2025
dc9df94
Merge pull request #2444 from farid-zare/develop
farid-zare Feb 18, 2025
d8a8b09
Merge branch 'opencobra:develop' into develop
bramnap Feb 24, 2025
0363c8c
Update mgPipe.m
bramnap Feb 24, 2025
8271f62
update Function Docs (Automatic Workflow)
bramnap Feb 24, 2025
61a9e20
Update mgPipe.m
bramnap Feb 24, 2025
79819dc
update Function Docs (Automatic Workflow)
bramnap Feb 24, 2025
1f406de
Update microbiotaModelSimulator.m
bramnap Feb 24, 2025
67ff46b
update Function Docs (Automatic Workflow)
bramnap Feb 24, 2025
5fa029b
Update mgPipe.m
farid-zare Feb 24, 2025
3733445
Update microbiotaModelSimulator.m
farid-zare Feb 24, 2025
3b118e3
update Function Docs (Automatic Workflow)
farid-zare Feb 24, 2025
44ac612
update Function Docs (Automatic Workflow)
farid-zare Feb 24, 2025
b2260e6
Merge pull request #2446 from bramnap/develop
farid-zare Feb 24, 2025
80847f4
Merge branch 'it_04_07_2024' of github.com:ithiele/cobratoolbox into …
ithiele Feb 24, 2025
beec534
Code base upload for Persephone publication
bramnap Feb 25, 2025
d609758
update Function Docs (Automatic Workflow)
bramnap Feb 25, 2025
73dbe17
Merge pull request #2447 from bramnap/develop
farid-zare Feb 25, 2025
0478293
Merge pull request #2376 from rmtfleming/develop
rmtfleming Mar 5, 2025
4978a98
Merge pull request #2385 from Sami990/master
rmtfleming Mar 5, 2025
0eabab2
Merge pull request #2424 from ithiele/it_04_07_2024
rmtfleming Mar 5, 2025
30d006a
update Function Docs (Automatic Workflow)
pavan-kumar-s Mar 9, 2025
989e0c0
updated the codes to remove docs folder and for CI/CD
pavan-kumar-s Mar 11, 2025
de48877
Merge pull request #2452 from pavan-kumar-s/develop
farid-zare Mar 11, 2025
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9 changes: 4 additions & 5 deletions .github/workflows/UpdateContributors.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,14 @@ name: Update Contributors list
on:
push:
branches:
- develop
- master

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
Expand All @@ -32,12 +31,12 @@ jobs:
run: |
python GenerateContributorsHTML.py

- name: Deploy to docs
- name: Deploy to gh-pages/stable
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: ./documentation/source/Contributions/contributors
publish_branch: develop
publish_branch: gh-pages
keep_files: true
destination_dir: docs
destination_dir: stable
commit_message: "Update Contributors (Automatic Workflow)"
15 changes: 7 additions & 8 deletions .github/workflows/UpdateFunctionDocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,14 @@ name: Update function docs
on:
push:
branches:
- develop
- master

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up Python 3.10
uses: actions/setup-python@v3
with:
Expand Down Expand Up @@ -50,26 +49,26 @@ jobs:
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: ./documentation/build/html/modules
branch: develop
target-folder: docs/modules
branch: gh-pages
target-folder: stable/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
publish_branch: gh-pages
keep_files: true
destination_dir: docs
destination_dir: stable
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
publish_branch: gh-pages
keep_files: true
destination_dir: docs/_static
destination_dir: stable/_static
commit_message: "update Function Docs (Automatic Workflow)"
7 changes: 4 additions & 3 deletions .github/workflows/UpdateTutorialIndex.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: Extract HTML Info

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

Expand All @@ -15,6 +15,7 @@ jobs:
with:
token: ${{ secrets.GITHUB_TOKEN }}
fetch-depth: 0
ref: gh-pages

- name: Check Commit Message
id: check_msg
Expand Down Expand Up @@ -45,7 +46,7 @@ jobs:
changed_files=$(git diff --name-only HEAD~1 HEAD | grep '\.html' | tr '\n' ' ')
for file in $changed_files; do
echo "Processing: $file"
python ./docs/extract_info.py $file
python ./stable/extract_info.py $file
done

- name: Commit and Push New File
Expand All @@ -55,4 +56,4 @@ jobs:
git config user.email "github-actions[bot]@users.noreply.github.com"
git add .
git commit -m "Update Tutorial (Automatic Workflow)" || echo "No changes to commit"
git push origin master
git push
2 changes: 1 addition & 1 deletion .github/workflows/testAllCI_step2.yml
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ jobs:
echo "PR_NUMBER=$PR_NUMBER" >> $GITHUB_ENV

- name: Publish Test Report
uses: ctrf-io/[email protected].6
uses: ctrf-io/[email protected].7
with:
report-path: 'artifacts/ctrf-report.json'
community-report: true
Expand Down
4 changes: 0 additions & 4 deletions docs/.buildinfo

This file was deleted.

85 changes: 0 additions & 85 deletions docs/.gitmodules

This file was deleted.

73 changes: 0 additions & 73 deletions docs/CITools/CheckTutorials.py.py

This file was deleted.

92 changes: 0 additions & 92 deletions docs/CITools/checkGhPages.py

This file was deleted.

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