Merge pull request #75 from KrishnaswamyLab/versions_and_release

Correcting actions to release a new pypi packages. The filing test are expected

Author: bjoaofelipe

.github/workflows/deploy.yml

@@ -14,19 +14,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
 
     - name: Install pypa/build
       run: >-
-        python -m
-        pip install
-        build
-        --user
+        python -m pip install build --user
 
     - name: Build a binary wheel and a source tarball
       run: >-

.github/workflows/pre-commit.yml

@@ -6,6 +6,10 @@ on:
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
 
+permissions:
+  contents: write
+  workflows: write 
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -23,19 +27,19 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Cache pre-commit
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
 
       - name: Run pre-commit
         id: precommit
-        uses: pre-commit/[email protected].0
+        uses: pre-commit/[email protected].1
         continue-on-error: true
 
       - name: Commit files
@@ -59,4 +63,4 @@ jobs:
 
       - name: Check pre-commit
         if: steps.precommit.outcome == 'failure'
-        uses: pre-commit/[email protected].0
+        uses: pre-commit/[email protected].1

.github/workflows/run_tests.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -40,12 +40,12 @@ jobs:
         sudo apt-get install -y libhdf5-dev libhdf5-serial-dev pandoc gfortran libblas-dev liblapack-dev llvm-dev
 
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.config.python }}
 
     - name: Cache Python packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
         key: ${{runner.os}}-${{ matrix.config.python }}-pip-${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
@@ -71,7 +71,7 @@ jobs:
 
     - name: Upload check results on fail
       if: failure()
-      uses: actions/upload-artifact@master
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ matrix.config.name }}_results
         path: check