Automated template update to v0.5.0

Author: scverse-bot

.bumpversion.cfg

@@ -1,17 +1,17 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                # Require 1% coverage, i.e., always succeed
-                target: 1
-        patch: false
-        changes: false
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
 
 comment:
-    layout: diff, flags, files
-    behavior: once
-    require_base: no
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.codecov.yaml

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "7b86b3572123c7777e012adcf6fff0c7217ba7a0",
-  "checkout": null,
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
   "context": {
     "cookiecutter": {
       "project_name": "FlowSOM",
@@ -10,13 +10,33 @@
       "author_full_name": "Artuur Couckuyt",
       "author_email": "[email protected]",
       "github_user": "artuurC",
-      "project_repo": "https://github.com/artuurC/FlowSOM",
+      "github_repo": "FlowSOM",
       "license": "GNU General Public License Version 3",
+      "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": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
     }
   },
   "directory": null

.cruft.json

@@ -8,5 +8,8 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.editorconfig

@@ -2,88 +2,93 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-    - type: markdown
-      attributes:
-          value: |
-              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
-              detailing how to provide the necessary information for us to reproduce your bug. In brief:
-                * Please provide exact steps how to reproduce the bug in a clean Python environment.
-                * In case it's not clear what's causing this bug, please provide the data or the data generation procecure.
-                * Sometimes it is not possible to share the data but usually it is possible to replicate problems on publicly
-                  available datasets or to share a subset of your data.
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
 
-    - type: textarea
-      id: report
-      attributes:
-          label: Report
-          description: A clear and concise description of what the bug is.
-      validations:
-          required: true
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
 
-    - type: textarea
-      id: versions
-      attributes:
-          label: Version information
-          description: |
-              Please paste below the output of
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
 
-              ```python
-              import session_info
-              session_info.show(html=False, dependencies=True)
-              ```
-          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
+        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_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        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

.flake8

@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
-    - name: Scverse Community Forum
-      url: https://discourse.scverse.org/
-      about: If you have questions about “How to do X”, please ask them here.
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,10 +2,10 @@ name: Feature request
 description: Propose a new feature for FlowSOM
 labels: enhancement
 body:
-    - type: textarea
-      id: description
-      attributes:
-          label: Description of feature
-          description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
-      validations:
-          required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true