Merge pull request #218 from mdshw5/master

Update develop

.coveragerc

@@ -5,8 +5,6 @@ omit =
     */lib_pypy/_*.py
     */site-packages/ordereddict.py
     */site-packages/nose/*
-    */site-packages/six/*
-    */unittest2/*
 
 [paths]
 source =

.github/workflows/main.yml

@@ -12,47 +12,76 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
+      fail-fast: false
+      max-parallel: 10
       matrix:
-        python: [3.7.12, 3.8.12, 3.9.10, 3.10.2]
+        python-version: ['3.11', '3.10', '3.9', '3.8', '3.7']
         os: [ubuntu-latest, macos-latest]
+        exclude:
+          # mac os: exclude all but the last two (available) python releases
+          - os: macos-latest
+            python-version: 3.8
+          - os: macos-latest
+            python-version: 3.7
+          # mac os: exclude python 3.11 since it's not yet available for runners
+          - os: macos-latest
+            python-version: 3.11
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v2.3.1 
+      - name: checkout
+        uses: actions/checkout@v3.1.0
         with:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: install macOS dependencies
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: brew install -q samtools bcftools xz
+
+      - name: setup python
+        uses: actions/setup-python@v4.3.0
         with:
           python-version: ${{ matrix.python }}
+
+      - name: upgrade pip
+        run: python3 -m pip install --upgrade pip
 
-      - name: Install python packages
-        run: pip install -r dev-requirements.txt
+      - name: pip install development dependencies
+        run: |
+          python3 -m pip install cython
+          python3 -m pip install -r dev-requirements.txt
           
-      - name: Install package
-        run: python setup.py install
+      - name: install pysam under Linux
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: python3 -m pip install pysam
+
+      - name: install pyfaidx from current branch
+        run: python3 -m pip install .
 
       - name: Cache test data
-        uses: actions/cache@v2
+        uses: actions/cache@v3.0.11
         with:
           path: tests/data
           key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('tests/data/*') }}
 
-      - name: Download test data
-        run: python tests/data/download_gene_fasta.py
+      - name: download test data
+        run: python3 tests/data/download_gene_fasta.py
 
-      - name: Run tests
+      - name: run pyfaidx tests
         run: pytest --cov=pyfaidx --cov-report=xml tests
 
-      - name: Run acidbio BED tests
+      - name: run acidbio tests
         run: |
           git clone https://github.com/mdshw5/acidbio.git
           cd acidbio/bed
           python3 -m pip install -r requirements.txt
           cp config_template.yaml config.yaml
           python3 bedrunall.py --tool pyfaidx BED03 ./
-                
-      - name: Codecov
-        uses: codecov/codecov-action@v2.1.0
+          
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        continue-on-error: true
+        with:
+          fail_ci_if_error: true
+          files: ./coverage.xml
+          verbose: true

.github/workflows/pypi.yml

@@ -1,37 +1,40 @@
 name: Package Builds
-on: push
+on:
+  release:
+    types: [published]
+  push:
+      branches:
+        - master
 
 jobs:
   build-n-publish:
-    name: Build and publish packages to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    name: build and publish packages to PyPI and TestPyPI
+    runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v2.3.1 
+      - name: checkout
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: setup python
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
 
-      - name: Install python packages
-        run: pip install setuptools
-
-      - name: Build package
-        run: python setup.py sdist
-
-      - name: Publish to test PyPI
-        uses: pypa/gh-action-pypi-publish@master
+      - name: build package
+        run: pipx run build
+
+      - name: publish to test PyPI
+        if: startsWith(github.ref, 'refs/tags') != true
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
             password: ${{ secrets.test_pypi_password }}
             repository_url: https://test.pypi.org/legacy/
 
-      - name: Publish to tagged release to PyPI
+      - name: publish tagged release to PyPI
         if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
             password: ${{ secrets.pypi_password }}

README.rst

@@ -1,4 +1,4 @@
-|CI| |Package| |PyPI| |Coverage| |Depsy|
+|CI| |Package| |PyPI| |Coverage| |Depsy| |Downloads|
 
 Description
 -----------
@@ -36,10 +36,12 @@ or download a `release <https://github.com/mdshw5/pyfaidx/releases>`_ and:
 
 ::
 
-    python setup.py install
+    pip install .
 
 If using ``pip install --user`` make sure to add ``/home/$USER/.local/bin`` to your ``$PATH`` (on linux) or ``/Users/$USER/Library/Python/{python version}/bin`` (on macOS) if you want to run the ``faidx`` script.
 
+Python 2.6 and 2.7 users may choose to use a package version from `v0.7.2 <https://github.com/mdshw5/pyfaidx/releases/tag/v0.7.2.2>`_ or earier.
+
 Usage
 -----
 
@@ -413,6 +415,9 @@ Examples:
 
 .. code:: bash
 
+    $ faidx -v tests/data/genes.fasta
+    ### Creates an .fai index, but supresses sequence output using --invert-match ###
+
     $ faidx tests/data/genes.fasta NM_001282543.1:201-210 NM_001282543.1:300-320
     >NM_001282543.1:201-210
     CTCGTTCCGC
@@ -643,3 +648,6 @@ Comprehensive Cancer Center in the Department of Oncology.
    
 .. |Package| image:: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml/badge.svg
    :target: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml
+   
+.. |Downloads| image:: https://img.shields.io/pypi/dm/pyfaidx.svg
+   :target: https://pypi.python.org/pypi/pyfaidx/

dev-requirements.txt

@@ -1,10 +1,8 @@
-six
 pytest
 pytest-cov
 setuptools
-mock
 cython 
-pysam 
+# pysam
 requests 
 coverage 
 pyfasta