updates from internal repository

.flake8

@@ -5,9 +5,10 @@ max_line_length = 120
 # B007: it can be intended to name loop variables even if they are not used
 # B023: leads to a lot of false alarms at the moment: https://github.com/PyCQA/flake8-bugbear/issues/269
 # B027: it is totally valid to prepare more methods in an abstract class without forcing them to be abstract
-# B028: currently broken: https://github.com/PyCQA/flake8-bugbear/issues/329
 # D*: pydocstyle has a lot of irrelevant checks by default. We are mainly interested in D417 (checks for missing arguments)
-ignore = B007, B023, B027, B028, C408, E203, E501, E721, E731, E741, W503, F841, D1, D200, D202, D205, D212, D400, D401, D402, D415
+ignore = B007, B023, B027, C408, E203, E501, E721, E731, E741, W503, F841, D1, D200, D202, D205, D212, D400, D401, D402, D415
 extend-select = B902, B904
 per_file_ignores = __init__.py: F401
-docstring-convention=google
+docstring-convention = google
+# rich has a print function which is explicitly named the same way for easy replacement
+builtins-ignorelist = print

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,21 +2,24 @@
 name: 🐛 Bug report
 about: Create a report to help us improve
 title: "[Bug]"
-labels: ''
-assignees: ''
-
+labels: ""
+assignees: ""
 ---
 
 ## :bug: Bug
+
 <!-- Thank you for taking the time to fill this bug report! -->
 
 ### Description
+
 <!-- Please describe the bug as concise as possible. What is the error message? Did you change something? -->
 
 ### Dataset
+
 Which dataset are you using? [`HeiPorSPECTRAL` | `private`]
 
 <!-- Anything else which could be relevant regarding the dataset? -->
 
 ### Environment
+
 <!-- Please run `htc info`, remove any private information and report the results here -->

.github/ISSUE_TEMPLATE/dataset.md

@@ -2,9 +2,8 @@
 name: 🌈 Dataset
 about: Everything related to the public HeiPorSPECTRAL dataset
 title: "[Dataset]"
-labels: ''
-assignees: ''
-
+labels: ""
+assignees: ""
 ---
 
 ## :rainbow: Dataset

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,10 +1,9 @@
 ---
 name: 🧗 Feature request
 about: Suggest an idea for this project
-title: '[Feature]'
-labels: ''
-assignees: ''
-
+title: "[Feature]"
+labels: ""
+assignees: ""
 ---
 
 ## :climbing: Feature

.github/ISSUE_TEMPLATE/question.md

@@ -2,9 +2,8 @@
 name: ❓ Question
 about: Ask a question
 title: "[Question]"
-labels: ''
-assignees: ''
-
+labels: ""
+assignees: ""
 ---
 
 ## :question: Question

.github/workflows/dataset.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - name: Checkout files
@@ -51,11 +51,11 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
+          cache: "pip"
 
       - name: Install htc package
         run: pip install imsy-htc
-      
+
       - name: Run example
         env:
           PATH_Tivita_HeiPorSPECTRAL: HeiPorSPECTRAL_example

.github/workflows/tests.yml

@@ -9,25 +9,25 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-        cache-dependency-path: 'requirements*.txt'
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+          cache-dependency-path: "requirements*.txt"
 
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install pytest wheel
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install pytest wheel
 
-    - name: Install htc
-      run: pip install --no-use-pep517 -e .
+      - name: Install htc
+        run: pip install --no-use-pep517 -e .
 
-    - name: Tests
-      run: py.test --doctest-modules --import-mode=importlib --collect-only .
+      - name: Tests
+        run: py.test --doctest-modules --import-mode=importlib --collect-only .

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # Order plays a role here: we first need to run pyupgrade because it changes the code and the new code may not be correctly formatted so we need to run black afterwards. flake8 again should be run after black so that it doesn't e.g. complain about whitespace issues.
 repos:
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: [--py39-plus]
@@ -22,6 +22,7 @@ repos:
           - flake8-comprehensions
           - flake8-use-pathlib
           - flake8-docstrings
+          - flake8-builtins
   - repo: https://github.com/asottile/yesqa
     rev: v1.5.0
     hooks:
@@ -31,8 +32,9 @@ repos:
           - flake8-comprehensions
           - flake8-use-pathlib
           - flake8-docstrings
+          - flake8-builtins
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
+    rev: 1.8.5
     hooks:
       - id: nbqa-pyupgrade
         args: [--py39-plus]
@@ -43,7 +45,14 @@ repos:
           - flake8-comprehensions
           - flake8-use-pathlib
           - flake8-docstrings
+          - flake8-builtins
         args: ["--extend-ignore=E402"]
+  # Avoid potential problems with py.test if __init__.py files are missing
+  - repo: https://github.com/lk16/detect-missing-init
+    rev: v0.1.6
+    hooks:
+      - id: detect-missing-init
+        args: ["--create", "--python-folders", "htc"]
   - repo: https://github.com/citation-file-format/cff-converter-python
     rev: "44e8fc9"
     hooks:
@@ -56,3 +65,36 @@ repos:
     rev: 1.7.0
     hooks:
       - id: pyproject-fmt
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-yaml
+      - id: check-toml
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: debug-statements
+      - id: name-tests-test
+        args: [--pytest-test-first]
+      - id: mixed-line-ending
+      - id: end-of-file-fixer
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+  - repo: local
+    hooks:
+      - id: check-notebooks
+        name: Check notebooks for common errors
+        entry: python hooks/check_notebooks.py
+        language: system
+        types: [jupyter]
+      - id: check-public-readme
+        name: Check for common mistakes in the public README
+        entry: python hooks/check_public_readme.py
+        language: system
+        types: [file]
+        files: ^README_public.md$
+  - repo: meta
+    hooks:
+      - id: check-hooks-apply
+      - id: check-useless-excludes

CITATION.cff

@@ -12,5 +12,5 @@ identifiers:
     value: 10.5281/zenodo.6577614
 repository-code: "https://github.com/IMSY-DKFZ/htc"
 license: MIT
-version: v0.0.15
-date-released: "2024-02-05"
+version: v0.0.16
+date-released: "2024-08-05"

LICENSES/MIT.txt

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.