Merge branch 'main' into v2.5.12-hotfix

.github/workflows/docs-mkdocs.yml

@@ -0,0 +1,25 @@
+name: docs
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "**.md"
+      - .github/workflows/docs-mkdocs.yml
+      - mkdocs.yml
+
+jobs:
+  mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/mkdocs-mike@main
+        with:
+          github-token: ${{ github.token }}

.github/workflows/draft-release.yml

@@ -3,7 +3,7 @@ name: draft-release
 on:
   workflow_dispatch:
     inputs:
-      version_tag:
+      version-tag:
         description: |
           Semantic version tag for next release.
           If not provided, it will be determined based on conventional commit history.
@@ -12,139 +12,14 @@ on:
         type: string
         default: ""
 
-env:
-  GH_TOKEN: ${{ github.token }}
-  BRANCH: release-draft
-
 jobs:
   draft-release:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # required to include tags
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - run: pip install cffconvert>=2.0.0 pyyaml
-
-      - name: Get Date
-        run: |
-          echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_ENV"
-
-      - name: Get current and next versions
-        id: semver
-        uses: ietf-tools/semver-action@v1
+      - uses: CCBR/actions/draft-release@v0.1
         with:
-          token: ${{ github.token }}
-          branch: ${{ github.ref_name }}
-
-      - name: Set version variables
-        shell: python {0}
-        run: |
-          import os
-          import re
-          import warnings
-
-          convco_version = "${{ steps.semver.outputs.next }}"
-          if "${{ github.event_name }}" == 'workflow_dispatch' and "${{ github.event.inputs.version_tag }}":
-            next_version = "${{ github.event.inputs.version_tag }}"
-            if next_version != convco_version:
-              warnings.warn(f"Manual version ({next_version}) not equal to version determined by conventional commit history ({convco_version})")
-          else:
-            next_version = convco_version
-
-          with open(os.getenv("GITHUB_ENV"), 'a') as out_env:
-            out_env.write(f"NEXT_VERSION={next_version}\n")
-            out_env.write(f"NEXT_STRICT={next_version.strip('v')}\n")
-          current_version = "${{ steps.semver.outputs.current }}"
-
-          # assert semantic version pattern
-          semver_pattern = 'v(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+(?P<buildmetadata>[0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?'
-          next_semver = re.match(semver_pattern, next_version)
-          if not next_semver:
-            extra_msg = ''
-            if not next_version.startswith('v'):
-              extra_msg = "The tag does not start with 'v'."
-            raise ValueError(f"Tag {next_version} does not match semantic versioning guidelines. {extra_msg}\nView the guidelines here: https://semver.org/")
-
-          # assert next version is only 1 greater than current
-          current_semver = re.match(semver_pattern, current_version)
-          groups = ['major', 'minor', 'patch']
-          greater = sum([next_semver.group(grp) > current_semver.group(grp) for grp in groups])
-          if not (greater == 1):
-            raise ValueError(f"Next version must only increment one number at a time. Current version: {current_version}. Proposed next version: {next_version}")
-
-      - name: Get release notes, update changelog & version file
-        shell: python {0}
-        run: |
-          import os
-          latest_version = "${{ steps.semver.outputs.current }}".strip('v')
-          next_version = "${{ env.NEXT_STRICT }}"
-
-          changelog_lines = list()
-          next_release_lines = list()
-          for_next = True
-          with open("CHANGELOG.md", "r") as infile:
-            for line in infile:
-              if line.startswith('#') and 'development version' in line:
-                line = line.replace('development version', next_version)
-              elif latest_version in line:
-                for_next = False
-
-              changelog_lines.append(line)
-              if for_next and next_version not in line:
-                next_release_lines.append(line)
-
-          with open(".github/latest-release.md", "w") as outfile:
-            outfile.writelines(next_release_lines)
-          with open('CHANGELOG.md', 'w') as outfile:
-            outfile.writelines(changelog_lines)
-          with open("VERSION", "w") as outfile:
-            outfile.write(f"{next_version}\n")
-
-      - name: Update citation
-        shell: python {0}
-        run: |
-          from cffconvert.cli.create_citation import create_citation
-          from cffconvert.cli.validate_or_write_output import validate_or_write_output
-          import yaml
-
-          citation = create_citation('CITATION.cff', None)
-          citation._implementation.cffobj['version'] = "${{ env.NEXT_VERSION }}"
-          citation._implementation.cffobj['date-released'] = "${{ env.DATE }}"
-          with open('CITATION.cff', 'w') as outfile:
-            outfile.write(yaml.dump(citation._implementation.cffobj, sort_keys=False, indent=2))
-
-      - uses: pre-commit/action@v3.0.0
-        with:
-          extra_args: --files CITATION.cff CHANGELOG.md VERSION
-        continue-on-error: true
-
-      - name: Commit & push to branch
-        run: |
-          git config --local user.name "github-actions[bot]"
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-
-          git push origin --delete ${{ env.BRANCH }} || echo "No ${{ env.BRANCH }} branch to delete"
-          git switch -c ${{ env.BRANCH }} || git switch ${{ env.BRANCH }}
-          git merge --ff-only ${{ github.ref_name }}
-
-          git add CITATION.cff CHANGELOG.md VERSION
-          git commit -m 'chore: prepare release ${{ env.NEXT_VERSION }}'
-          git push --set-upstream origin ${{ env.BRANCH }}
-
-          echo "COMMIT_HASH=$(git rev-parse HEAD)" >> "$GITHUB_ENV"
-
-      - name: Tag & draft release
-        run: |
-          gh release create ${{ env.NEXT_VERSION }} \
-            --draft \
-            --notes-file .github/latest-release.md \
-            --target ${{ env.COMMIT_HASH }} \
-            --title "${{ github.event.repository.name }} ${{ env.NEXT_STRICT }}"
-
-      - name: Next steps
-        run: |
-          echo "Next steps: Take a look at the changes in the ${{ env.BRANCH }} branch and the release notes on the web. If everything is correct, publish the release. Otherwise, delete the release draft and cut the release manually."
+          github-token: ${{ github.token }}
+          version-tag: ${{ github.event.inputs.version-tag }}

.github/workflows/main.yaml

@@ -9,28 +9,29 @@ on:
   pull_request:
 
 jobs:
-  Dryrun_Lint:
+  dryrun-lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: docker://snakemake/snakemake:v5.24.2
-      - name: Dry-run pipeline
+      - uses: docker://snakemake/snakemake:v7.32.4
+      - name: Dry-run
         run: |
-          docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v5.24.2 \
-            python src/renee/__main__.py run \
+          docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v7.32.4 \
+            ./bin/renee run \
               --input .tests/KO_S3.R1.fastq.gz .tests/KO_S3.R2.fastq.gz .tests/KO_S4.R1.fastq.gz .tests/KO_S4.R2.fastq.gz .tests/WT_S1.R1.fastq.gz .tests/WT_S1.R2.fastq.gz .tests/WT_S2.R1.fastq.gz .tests/WT_S2.R2.fastq.gz \
               --output output \
               --genome config/genomes/biowulf/hg38_30.json \
               --shared-resources .tests/shared_resources/ \
               --mode local \
               --dry-run
-      - name: Lint workflow
+      - name: Lint
         continue-on-error: true
         run: |
-          docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
+          docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
+            snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
           echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
 
-  Test:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -57,6 +58,10 @@ jobs:
           ./bin/renee --help
           ./bin/renee --version
         shell: micromamba-shell {0}
+      - name: pip install python package
+        run: |
+          pip install .[dev,test]
+        shell: micromamba-shell {0}
       - name: Test
         run: |
           python -m pytest
@@ -66,7 +71,7 @@ jobs:
 
   build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
     runs-on: ubuntu-latest
-    needs: [Dryrun_Lint, Test]
+    needs: [dryrun-lint, test]
     if: always()
     steps:
       - name: Successful build

.github/workflows/post-release.yml

@@ -5,52 +5,13 @@ on:
     types:
       - published
 
-env:
-  GH_TOKEN: ${{ github.token }}
-  BRANCH: release/${{ github.ref_name }}
-
 jobs:
   cleanup:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Configure git
-        run: |
-          git config --local user.name "github-actions[bot]"
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git push origin --delete ${{ env.BRANCH }} || echo "No ${{ env.BRANCH }} branch to delete"
-          git switch -c ${{ env.BRANCH }}
-      - name: Bump changelog & version
-        shell: python {0}
-        run: |
-          with open("CHANGELOG.md", "r") as infile:
-            lines = infile.readlines()
-          lines.insert(0, "## ${{ github.event.repository.name }} development version\n\n")
-          with open("CHANGELOG.md", "w") as outfile:
-            outfile.writelines(lines)
-
-          with open('VERSION', 'r') as infile:
-            version = infile.read().strip()
-          with open('VERSION', 'w') as outfile:
-            outfile.write(f"{version}-dev\n")
-
-      - uses: pre-commit/action@v3.0.0
+      - uses: CCBR/actions/post-release@v0.1
         with:
-          extra_args: --files CITATION.cff CHANGELOG.md VERSION
-        continue-on-error: true
-
-      - name: Open pull request
-        run: |
-          git add CHANGELOG.md VERSION
-          git commit -m "chore: bump changelog & version after release of ${{ github.ref_name }}"
-          git push --set-upstream origin ${{ env.BRANCH }}
-
-          gh pr create \
-            --fill-first \
-            --reviewer ${{ github.triggering_actor }}
-
-      - name: Clean up release-draft branch
-        run: |
-          git push origin --delete release-draft || echo "No release-draft branch to delete"
+          github-token: ${{ github.token }}

.github/workflows/techdev-project.yml

@@ -0,0 +1,18 @@
+name: Add issues/PRs to the TechDev project
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@v1.0.2
+        with:
+          project-url: https://github.com/orgs/CCBR/projects/17
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

CHANGELOG.md

@@ -1,3 +1,23 @@
+## RENEE development version
+
+### New features
+
+- Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
+- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
+- Add `renee gui` subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
+  - Previously, `renee_gui` (with an underscore) was a command in the `ccbrpipeliner` module.
+
+### Bug fixes
+
+- Ensure `renee build` creates necessary `config` directory during initialization. (#139, @kelly-sovacool)
+
+### Documentation updates
+
+- Minor documentation improvements. (#132, #135, #152, @kelly-sovacool)
+- Add GUI instructions to the documentation website. (#38, @samarth8392)
+- The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
+- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
+
 ## RENEE 2.5.12
 
 - Minor documentation improvements. (#100, @kelly-sovacool)