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Conda lock files #5827

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Conda lock files #5827

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dbad13e
ci(#2193): Add condalock file generation
edmundmiller Jun 18, 2024
6ea762d
ci: Add write permissions
edmundmiller Jun 18, 2024
b740f85
ci: Add gh pr checkout
edmundmiller Jun 18, 2024
95ba6cc
ci: Try a pre-canned action
edmundmiller Jun 18, 2024
07a250e
ci: Cut out conda-lock-refresh
edmundmiller Jun 18, 2024
b3ef764
ci: Use plain GITHUB_TOKEN secret
edmundmiller Jun 18, 2024
98cbce3
ci: Skip committing
edmundmiller Jun 18, 2024
253a398
ci: Use Commit step from prettier linting
edmundmiller Aug 8, 2024
f085cc1
ci: Try actions/checkout#719
edmundmiller Aug 8, 2024
fe828fa
ci: Clean up commit message
edmundmiller Aug 8, 2024
8433c87
ci: Output lock file to the directory
edmundmiller Aug 8, 2024
a9f4d26
chore: Update an environment file for testing
edmundmiller Aug 8, 2024
22c4985
[automated] autogenerated conda-lock file
nf-core-bot Aug 8, 2024
3afecb6
ci: Clean up the matrix to avoid a race condition
edmundmiller Aug 8, 2024
c6b7ae6
style: Ignore conda-lock for prettier
edmundmiller Aug 8, 2024
251b8ca
ci: Allow no conda-lock updates
edmundmiller Aug 8, 2024
de2fdf7
build: Try a conda-lock file
edmundmiller Aug 9, 2024
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87 changes: 87 additions & 0 deletions .github/workflows/wave.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
name: Generate conda-lock
# When environment.yml is changed
on:
pull_request:
paths:
- "**/environment.yml"

jobs:
gen-matrix:
name: generate-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4

- name: Calculate file differences
id: diff
uses: tj-actions/changed-files@v44
with:
json: true
quotepath: false
files: |
modules/**/environment.yml
- name: Debug
run: echo ${{ steps.diff.outputs.all_changed_files }}
- id: set-matrix
run: echo "matrix={\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"

outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}

lock:
if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
needs: gen-matrix
name: Generate conda-lock file
permissions:
contents: write
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
steps:
- uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
with:
ref: ${{ github.event.pull_request.head.ref }}

- uses: mamba-org/setup-micromamba@v1
with:
environment-name: conda-lock-env
create-args: >-
python=3.11
conda-lock
mamba

- name: Get the lock file path
uses: actions/github-script@v7
id: lockfile-name
with:
result-encoding: string
script: |
return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml');

- name: Run conda-lock
run: |
rm --force "${{steps.lockfile-name.outputs.result}}"
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}"
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@pinin4fjords pinin4fjords Aug 12, 2024 •
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So, I tested why the lock file didn't work, and I think it's because of the default unified lock files. To get a lock file compatible with Nextflow (which just does like this), you have to render it to a platform specific one:

conda-lock render -p osx-64  
Rendering lockfile(s) for osx-64...
 - Install lock using : conda create --name YOURENV --file conda-osx-64.lock

We can also just do:

conda-lock --kind explicit -f environment.yml

... which automatically renders to all the specified platforms.

In any case, for nextflow as-is, we will need platform-specific lockfiles.

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Awesome! I didn't really want to have 4+ lock files floating around. I didn't know this was a possibility, great find!

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I'm afraid we're stuck with those 4 lock files, unless we do that rendering dynamically somehow.

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Suggested change
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}"
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind explicit --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}"
mv conda-linux-64.lock conda-lock-linux-64.yml

Nextflow needs it to be a .yml, but use of --kind explicit means we get .lock files, so we'll need to do some file renaming.

Platforms should probably be set in the environment.ymls actually.

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Can we just do...

Suggested change
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}"
conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}".yml

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Doesn't look like that works 😞

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The explicit thing is important. It makes you a lock file for each platform which is consumable by conda env create, and therefore by Nextflow.

But by doing explicit you lose control over the naming of the multiple outputs, and Nextflow needs .yml, hence the rename hack I suggested.

env:
MAMBA: "--mamba"
shell: bash -l {0}

- name: Commit & push changes
id: commit-and-push
run: |
git config user.email "core@nf-co.re"
git config user.name "nf-core-bot"
git config push.default upstream
git add .
git status
git commit -m "[automated] autogenerated conda-lock file"
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Suggested change
git commit -m "[automated] autogenerated conda-lock file"
git commit -m "[automated] autogenerated conda-lock files"

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It should just be a single commit per lock file I think?

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One lock file per platform

git push

- name: If no conda-lock update
if: steps.commit-and-push.outcome == 'failure'
run: |
echo "No conda-lock update"

# TODO Build containers with Wave
1 change: 1 addition & 0 deletions .prettierignore
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Original file line number Diff line number Diff line change
Expand Up @@ -15,3 +15,4 @@ __pycache__
*.pyo
*.pyc
.github/renovate.json5
**/conda-lock.yml
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Suggested change
**/conda-lock.yml
**/conda-lock*.yml

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