Code release v0.2.0

.github/workflows/pre-commit.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.9"]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3

.github/workflows/unit-test.yml

@@ -1,24 +1,18 @@
 name: unit-test
 
 on:
-  schedule:
-    - cron: "0 0 * * *"
-  workflow_dispatch:
-  # Trigger the workflow on push or pull request,
-  # but only for the main branch
-  push:
-    branches:
-      - main
   pull_request:
-    branches:
-      - main
+  push:
+    branches: [main]
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
+    timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ["3.8"]
+        group: [1, 2, 3, 4]
+        python-version: ["3.9"]
 
     steps:
       - name: Checkout repository
@@ -37,11 +31,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tensorflow-cpu==2.11.0
-          pip install jax==0.4.1
-          pip install jaxlib==0.4.1
+          pip install tensorflow-cpu==2.12.0
+          pip install jax==0.4.8
+          pip install jaxlib==0.4.7
           pip install -r docker/requirements.txt
-          pip install -e .
+          pip install -e imgx
+          pip install -e imgx_datasets
       - name: Test with pytest
         run: |
-          pytest tests/unit
+          pytest --splits 4 --group ${{ matrix.group }} --randomly-seed=0 -k "not slow" imgx/tests/unit
+          pytest --splits 4 --group ${{ matrix.group }} --randomly-seed=0 -k "not slow" imgx_datasets/tests

.pre-commit-config.yaml

@@ -27,15 +27,37 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.7.0
     hooks:
       - id: black
         args:
           - --line-length=80
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
-    hooks:
+    rev: v1.4.1
+    hooks: # https://github.com/python/mypy/issues/4008#issuecomment-582458665
+      - id: mypy
+        name: mypy-imgx
+        files: ^imgx/
+        entry: mypy imgx/
+        pass_filenames: false
+        args:
+          [
+            --strict-equality,
+            --disallow-untyped-calls,
+            --disallow-untyped-defs,
+            --disallow-incomplete-defs,
+            --check-untyped-defs,
+            --disallow-untyped-decorators,
+            --warn-redundant-casts,
+            --warn-unused-ignores,
+            --no-warn-no-return,
+            --warn-unreachable,
+          ]
       - id: mypy
+        name: mypy-imgx_datasets
+        files: ^imgx_datasets/
+        entry: mypy imgx_datasets/
+        pass_filenames: false
         args:
           [
             --strict-equality,
@@ -50,29 +72,27 @@ repos:
             --warn-unreachable,
           ]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+    rev: v3.0.0
     hooks:
       - id: prettier
         args:
           - --print-width=80
           - --prose-wrap=always
           - --tab-width=2
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.254"
+    rev: "v0.0.280"
     hooks:
       - id: ruff
   - repo: https://github.com/pre-commit/mirrors-pylint
     rev: v3.0.0a5
     hooks:
       - id: pylint
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.9.0
     hooks:
       - id: pyupgrade
         args:
-          - --py36-plus
-          - --py37-plus
-          - --py38-plus
+          - --py39-plus
   - repo: https://github.com/pycqa/pydocstyle
     rev: 6.3.0
     hooks:

Makefile

@@ -0,0 +1,19 @@
+pip:
+	pip install -e imgx
+	pip install -e imgx_datasets
+
+test:
+	pytest --cov=imgx -n 4 imgx/tests -x
+	pytest --cov=imgx_datasets -n 4 imgx_datasets/tests -x
+
+build_dataset:
+	tfds build imgx_datasets/imgx_datasets/male_pelvic_mr &
+	tfds build imgx_datasets/imgx_datasets/amos_ct &
+	tfds build imgx_datasets/imgx_datasets/muscle_us &
+	tfds build imgx_datasets/imgx_datasets/brats2021_mr &
+
+rebuild_dataset:
+	tfds build imgx_datasets/imgx_datasets/male_pelvic_mr --overwrite &
+	tfds build imgx_datasets/imgx_datasets/amos_ct --overwrite &
+	tfds build imgx_datasets/imgx_datasets/muscle_us --overwrite &
+	tfds build imgx_datasets/imgx_datasets/brats2021_mr --overwrite &