Merge pull request #111 from bigbio/dev

remove unnecesary tests

Author: ypriverol

.github/workflows/pytest.yml

@@ -12,24 +12,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v4
       with:
         lfs: true
-    
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest pytest-cov
         pip install .
-    
+
     - name: Verify test data files
       run: |
         ls -la tests/resources/maxquant/PXD003133-22min/
@@ -39,11 +39,11 @@ jobs:
         else
           echo "Test data files found."
         fi
-    
+
     - name: Test with pytest
       run: |
         pytest tests/ -v --cov=pmultiqc
-    
+
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       with:

.github/workflows/python-app.yml

@@ -111,10 +111,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Install package
         run: pip install .
       - name: Test mzid & mzML file
@@ -136,10 +136,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python "3.10"
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Install package
         run: pip install .
       - name: Test mzid & MGF file
@@ -163,10 +163,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python "3.10"
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Install package
         run: pip install .
       - name: Test MaxQuant file

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/python-publish.yml

@@ -26,7 +26,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -37,4 +37,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/update_examples.yml

@@ -0,0 +1,37 @@
+name: Auto update exmaples
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  update_examples:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov
+          pip install .
+
+      - name: Update Examples Script
+        run: |
+          python docs/update_examples.py
+
+      - name: Push Results
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
+          git add .
+          git commit -m "Update exmaples"
+          git push

.gitignore

@@ -133,4 +133,5 @@ dmypy.json
 
 .idea
 /quantms.db
-/results_mq/
+/results_mq/
+.qodo

README.md

@@ -146,14 +146,7 @@ pmultiqc generates a comprehensive report with multiple sections:
 
 ## Example Reports
 
-You can find example reports in the `docs` directory:
-
-- [LFQ Example](docs/example_lfq/multiqc_report.html)
-- [TMT Example](docs/example_tmt/multiqc_report.html)
-- [DIA Example](docs/example_dia/multiqc_report.html)
-- [MaxQuant Example](docs/example_maxquant/multiqc_report.html)
-- [mzIdentML with mzML Example](docs/example_mzid_mzml/multiqc_report.html)
-- [mzIdentML with MGF Example](docs/example_mzid_mgf/multiqc_report.html)
+You can find example reports on the [docs page](https://bigbio.github.io/pmultiqc).
 
 ## Development