Merge branch 'dev' into 2865-fix-schema-docs-console-printing

nf-core · Mar 19, 2024 · 629e85e · 629e85e
2 parents fa6504b + cdd5f43
commit 629e85e
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -37,5 +37,5 @@ body:
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.10, 3.11)_
+        * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
+        * Python version _(eg. 3.11, 3.12)_
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -38,7 +38,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install packages
         run: |
@@ -64,10 +64,10 @@ jobs:
           git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV
           echo "File changed: ${{ env.changed }}"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -52,10 +52,10 @@ jobs:
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: pip
 
       - name: Install python dependencies

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -64,10 +64,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -51,10 +51,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -34,7 +34,7 @@ jobs:
       # Install and run pre-commit
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -20,10 +20,10 @@ jobs:
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -40,7 +40,7 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
           - python-version: "3.8"
@@ -159,12 +159,12 @@ jobs:
           cd pytest
 
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install dependencies

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -56,10 +56,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install python dependencies
         run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))
 - Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848))
 - Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849))
+- Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))
 
 ### Linting
 
@@ -38,6 +39,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.3 ([#2850](https://github.com/nf-core/tools/pull/2850))
 - Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))
 - Fix schema docs console output truncating ([#2880](https://github.com/nf-core/tools/pull/2880))
+- fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
-FROM python:3.11-slim@sha256:a2eb07f336e4f194358382611b4fea136c632b40baa6314cb27a366deeaf0144
-LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
-    description="Docker image containing requirements for the nfcore tools"
+FROM python:3.12-slim
+LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
+    description="Docker image containing requirements for nf-core/tools"
 
 # Do not pick up python packages from $HOME
 ENV PYTHONNUSERSITE=1

diff --git a/README.md b/README.md
@@ -82,7 +82,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.11 nf-core nextflow
+conda create --name nf-core python=3.12 nf-core nextflow
 conda activate nf-core
 ```
 

diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -37,7 +37,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:

diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -34,7 +34,7 @@ jobs:
       # Install and run pre-commit
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -16,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit
@@ -39,7 +39,7 @@ jobs:
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies

diff --git a/nf_core/schema.py b/nf_core/schema.py
@@ -582,7 +582,7 @@ def make_skeleton_schema(self):
         )
         schema_template = env.get_template("nextflow_schema.json")
         template_vars = {
-            "name": self.pipeline_manifest.get("name", Path(self.schema_filename).parent).strip("'"),
+            "name": self.pipeline_manifest.get("name", str(Path(self.schema_filename).parent)).strip("'"),
             "description": self.pipeline_manifest.get("description", "").strip("'"),
         }
         self.schema = json.loads(schema_template.render(template_vars))