fix merge conflict

.github/dependabot.yml

@@ -5,5 +5,3 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    ignore:
-      - dependency-name: "actions/*"

.github/workflows/distribution.yml

@@ -13,14 +13,14 @@ jobs:
   dist:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Build SDist and wheel
       run: pipx run build
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         path: dist/*
 
@@ -33,7 +33,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: artifact
         path: dist

.github/workflows/main.yml

@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  TQDM_MININTERVAL: 100
+
 jobs:
 
   build-and-test:
@@ -24,9 +27,9 @@ jobs:
         os: [ubuntu-latest, macOS-latest]
 
     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: Get dependencies and install the package
@@ -35,16 +38,16 @@ jobs:
         python -m pip install --upgrade .[test]
     - name: Run unit tests
       run: |
-        pytest
+        python -m pytest
 
   test-coverage:
     name: Calculate and upload test coverage
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -54,7 +57,7 @@ jobs:
           python -m pip install --upgrade .[test]
           python -m pytest --cov=pygama --cov-report=xml
       - name: Upload Coverage to codecov.io
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
@@ -63,10 +66,10 @@ jobs:
     name: Build documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: Setup build environment

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 exclude: ^(attic|tutorials|src/pygama/math|src/pygama/flow/datagroup.py)
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v4.4.0"
+  rev: "v4.5.0"
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -26,35 +26,35 @@ repos:
   - id: trailing-whitespace
 
 - repo: https://github.com/asottile/setup-cfg-fmt
-  rev: "v2.4.0"
+  rev: "v2.5.0"
   hooks:
   - id: setup-cfg-fmt
 
 - repo: https://github.com/PyCQA/isort
-  rev: "5.12.0"
+  rev: "5.13.2"
   hooks:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: "v3.13.0"
+  rev: "v3.15.0"
   hooks:
   - id: pyupgrade
     args: ["--py38-plus"]
 
 - repo: https://github.com/psf/black
-  rev: "23.9.1"
+  rev: "23.12.1"
   hooks:
   - id: black-jupyter
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v1.5.1"
+  rev: "v1.8.0"
   hooks:
   - id: mypy
     files: src
     stages: [manual]
 
 - repo: https://github.com/hadialqattan/pycln
-  rev: "v2.2.2"
+  rev: "v2.4.0"
   hooks:
   - id: pycln
     exclude: ^src/pygama/pargen
@@ -85,7 +85,7 @@ repos:
     stages: [manual]
 
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.5"
+  rev: "v2.2.6"
   hooks:
   - id: codespell
 
@@ -103,7 +103,7 @@ repos:
   - id: rst-inline-touching-normal
 
 - repo: https://github.com/pre-commit/mirrors-prettier
-  rev: "v3.0.3"
+  rev: "v4.0.0-alpha.8"
   hooks:
     - id: prettier
       types_or: [json]

README.md

@@ -1,3 +1,5 @@
+<img src=".github/logo.png" alt="pygama logo" align="left" height="150">
+
 # pygama
 
 [![PyPI](https://img.shields.io/pypi/v/pygama?logo=pypi)](https://pypi.org/project/pygama/)
@@ -25,3 +27,8 @@
 - generating and selecting high-level event data for further analysis
 
 Check out the [online documentation](https://pygama.readthedocs.io).
+
+## Related repositories
+- [legend-exp/legend-pydataobj](https://github.com/legend-exp/legend-pydataobj) → LEGEND Python Data Objects
+- [legend-exp/legend-daq2lh5](https://github.com/legend-exp/legend-daq2lh5) → Convert digitizer data to LEGEND HDF5
+- [legend-exp/dspeed](https://github.com/legend-exp/dspeed) → Fast Digital Signal Processing for particle detector signals in Python

docs/source/conf.py

@@ -39,6 +39,7 @@
     "source_directory": "docs/source",
 }
 html_title = f"{project} {version}"
+html_logo = "../../.github/logo.png"
 
 # sphinx-napoleon
 # enforce consistent usage of NumPy-style docstrings
@@ -57,9 +58,11 @@
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "pandas": ("https://pandas.pydata.org/docs", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
-    "iminuit": ("https://iminuit.readthedocs.io/en/stable", None),
     "h5py": ("https://docs.h5py.org/en/stable", None),
     "pint": ("https://pint.readthedocs.io/en/stable", None),
+    "lgdo": ("https://legend-pydataobj.readthedocs.io/en/stable", None),
+    "dspeed": ("https://dspeed.readthedocs.io/en/stable", None),
+    "daq2lh5": ("https://legend-daq2lh5.readthedocs.io/en/stable", None),
 }
 
 suppress_warnings = [