Data read improvements

.github/workflows/Coverage.yaml

@@ -1,35 +1,51 @@
 name: Coverage
 
 on:
-  - push
-  - pull_request
+  push:
+    branches: [main]
+    tags: ["v*"]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.head.sha || github.sha }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
   coverage:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 45
     strategy:
       matrix:
         os: [macos-14]
         python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
       - name: Install dependencies
         run: |
           if [ "$RUNNER_OS" = "Linux" ]; then
-            sudo apt update
-            sudo apt install -y libmpich-dev zlib1g-dev
+            sudo apt-get update
+            sudo apt-get install -y libmpich-dev zlib1g-dev
           elif [ "$RUNNER_OS" = "macOS" ]; then
+            brew update
             brew install mpich zlib
           fi
           python -m pip install --upgrade pip
           pip install tox tox-gh-actions
+
       - name: Run coverage
         run: tox -e coverage
+
       - name: Upload coverage report
         uses: actions/upload-artifact@v4
         with:

.github/workflows/format.yaml

@@ -1,32 +1,47 @@
 name: Format Check
 
 on:
-  - push
-  - pull_request
+  push:
+    branches: [main]
+    tags: ["v*"]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.head.sha || github.sha }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
   black:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
       matrix:
         os: [macos-14]
         python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
       - name: Install dependencies
         run: |
           if [ "$RUNNER_OS" = "Linux" ]; then
-            sudo apt update
-            sudo apt install -y libmpich-dev zlib1g-dev
+            sudo apt-get update
+            sudo apt-get install -y libmpich-dev zlib1g-dev
           elif [ "$RUNNER_OS" = "macOS" ]; then
+            brew update
             brew install mpich zlib
           fi
           python -m pip install --upgrade pip
           pip install tox tox-gh-actions
+
       - name: Run black
         run: tox -e black

.github/workflows/lint.yml

@@ -1,34 +1,47 @@
 name: Lint
 
 on:
-  - push
-  - pull_request
+  push:
+    branches: [main]
+    tags: ["v*"]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.head.sha || github.sha }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
   lint:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
       matrix:
         os: [macos-14]
         python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install MPI
+          cache: "pip"
+
+      - name: Install dependencies
         run: |
           if [ "$RUNNER_OS" = "Linux" ]; then
-            sudo apt update
-            sudo apt install -y libmpich-dev zlib1g-dev
+            sudo apt-get update
+            sudo apt-get install -y libmpich-dev zlib1g-dev
           elif [ "$RUNNER_OS" = "macOS" ]; then
+            brew update
             brew install mpich zlib
           fi
-      - name: Install dependencies
-        run: |
           python -m pip install --upgrade pip
           pip install tox tox-gh-actions
+
       - name: Run linter
         run: tox -e lint

.github/workflows/tests.yml

@@ -2,11 +2,22 @@ name: Tests
 
 on:
   push:
+    branches: [main]
+    tags: ["v*"]
   pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.head.sha || github.sha }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
@@ -15,35 +26,28 @@ jobs:
         mpi: [mpich, openmpi]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Cache pip
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: "pip"
 
       - name: Install MPI
         run: |
           if [ "$RUNNER_OS" = "Linux" ]; then
             sudo apt update
             if [ "${{ matrix.mpi }}" = "mpich" ]; then
               sudo apt install -y mpich libmpich-dev zlib1g-dev
-            elif [ "${{ matrix.mpi }}" = "openmpi" ]; then
+            else
               sudo apt install -y openmpi-bin libopenmpi-dev zlib1g-dev
             fi
-          elif [ "$RUNNER_OS" = "macOS" ]; then
+          else
             brew update
             if [ "${{ matrix.mpi }}" = "mpich" ]; then
               brew install mpich zlib
-            elif [ "${{ matrix.mpi }}" = "openmpi" ]; then
+            else
               brew install open-mpi zlib
             fi
           fi

.github/workflows/typecheck.yaml

@@ -1,32 +1,47 @@
 name: Type Check
 
 on:
-  - push
-  - pull_request
+  push:
+    branches: [main]
+    tags: ["v*"]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.head.sha || github.sha }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
   mypy:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
       matrix:
         os: [macos-14]
         python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
       - name: Install dependencies
         run: |
           if [ "$RUNNER_OS" = "Linux" ]; then
-            sudo apt update
-            sudo apt install -y libmpich-dev zlib1g-dev
+            sudo apt-get update
+            sudo apt-get install -y libmpich-dev zlib1g-dev
           elif [ "$RUNNER_OS" = "macOS" ]; then
+            brew update
             brew install mpich zlib
           fi
           python -m pip install --upgrade pip
           pip install tox tox-gh-actions
+
       - name: Run mypy
         run: tox -e mypy

MANIFEST.in

@@ -1,4 +1,5 @@
 include README.md
 include LICENSE
 recursive-include examples *
-recursive-include src/ *.pyx *.pxd *.py *.hpp *.h
+recursive-include src/ *.pyx *.pxd *.py *.hpp *.h
+recursive-include extern/ *.h