Update template to v0.6.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "f25cfb52557bd87017094a129d403b284b6dbba1",
-  "checkout": null,
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "binsparse",
@@ -10,13 +10,33 @@
       "author_full_name": "Isaac Virshup",
       "author_email": "[email protected]",
       "github_user": "ivirshup",
-      "project_repo": "https://github.com/ivirshup/binsparse",
+      "github_repo": "binsparse",
       "license": "MIT License",
+      "ide_integration": true,
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null

.editorconfig

@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -23,67 +23,72 @@ body:
   - type: textarea
     id: versions
     attributes:
-      label: Version information
+      label: Versions
       description: |
-        Please paste below the output of
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
 
         ```python
-        import session_info
-        session_info.show(html=False, dependencies=True)
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
         ```
+      render: python
       placeholder: |
-        -----
-        anndata             0.8.0rc2.dev27+ge524389
-        session_info        1.0.0
-        -----
-        asttokens           NA
-        awkward             1.8.0
-        backcall            0.2.0
-        cython_runtime      NA
-        dateutil            2.8.2
-        debugpy             1.6.0
-        decorator           5.1.1
-        entrypoints         0.4
-        executing           0.8.3
-        h5py                3.7.0
-        ipykernel           6.15.0
-        jedi                0.18.1
-        mpl_toolkits        NA
-        natsort             8.1.0
-        numpy               1.22.4
-        packaging           21.3
-        pandas              1.4.2
-        parso               0.8.3
-        pexpect             4.8.0
-        pickleshare         0.7.5
-        pkg_resources       NA
-        prompt_toolkit      3.0.29
-        psutil              5.9.1
-        ptyprocess          0.7.0
-        pure_eval           0.2.2
-        pydev_ipython       NA
-        pydevconsole        NA
-        pydevd              2.8.0
-        pydevd_file_utils   NA
-        pydevd_plugins      NA
-        pydevd_tracing      NA
-        pygments            2.12.0
-        pytz                2022.1
-        scipy               1.8.1
-        setuptools          62.5.0
-        setuptools_scm      NA
-        six                 1.16.0
-        stack_data          0.3.0
-        tornado             6.1
-        traitlets           5.3.0
-        wcwidth             0.2.5
-        zmq                 23.1.0
-        -----
-        IPython             8.4.0
-        jupyter_client      7.3.4
-        jupyter_core        4.10.0
-        -----
-        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
-        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
-        -----
-        Session information updated at 2022-07-07 17:55
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

.github/workflows/build.yaml

@@ -10,20 +10,24 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
 jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          cache-dependency-glob: pyproject.toml
       - name: Build package
-        run: python -m build
+        run: uv build
       - name: Check package
-        run: twine check --strict dist/*.whl
+        run: uvx twine check --strict dist/*.whl

.github/workflows/release.yaml

@@ -1,30 +1,34 @@
 name: Release
 
 on:
-  push:
-    tags:
-      - "*.*.*"
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
 
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
   release:
-    name: Release
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/binsparse
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
         with:
-          python-version: "3.10"
-
-      - name: Install hatch
-        run: pip install hatch
-
-      - name: Build project for distribution
-        run: hatch build
-
-      - name: Publish a Python distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1