Skip to content

Commit 7dc115b

Browse files
berombauberombau
authored
Merge pull request #20 from scverse-bot/template-update-v2-saeyslab-FlowSOM_Python
Update template to v0.5.0
2 parents 772f66a + 0be5e2c commit 7dc115b

24 files changed

+538
-372
lines changed

‎.cruft.json‎

Lines changed: 18 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
{
22
"template": "https://github.com/scverse/cookiecutter-scverse",
3-
"commit": "009f1b5205d007026e76b3dd79f57ad946947ceb",
4-
"checkout": null,
3+
"commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
4+
"checkout": "v0.5.0",
55
"context": {
66
"cookiecutter": {
77
"project_name": "FlowSOM",
@@ -10,19 +10,33 @@
1010
"author_full_name": "Artuur Couckuyt",
1111
"author_email": "[email protected]",
1212
"github_user": "artuurC",
13-
"project_repo": "https://github.com/artuurC/FlowSOM",
13+
"github_repo": "FlowSOM",
1414
"license": "GNU General Public License Version 3",
15+
"ide_integration": true,
1516
"_copy_without_render": [
1617
".github/workflows/build.yaml",
1718
".github/workflows/test.yaml",
1819
"docs/_templates/autosummary/**.rst"
1920
],
21+
"_exclude_on_template_update": [
22+
"CHANGELOG.md",
23+
"LICENSE",
24+
"README.md",
25+
"docs/api.md",
26+
"docs/index.md",
27+
"docs/notebooks/example.ipynb",
28+
"docs/references.bib",
29+
"docs/references.md",
30+
"src/**",
31+
"tests/**"
32+
],
2033
"_render_devdocs": false,
2134
"_jinja2_env_vars": {
2235
"lstrip_blocks": true,
2336
"trim_blocks": true
2437
},
25-
"_template": "https://github.com/scverse/cookiecutter-scverse"
38+
"_template": "https://github.com/scverse/cookiecutter-scverse",
39+
"_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
2640
}
2741
},
2842
"directory": null

‎.editorconfig‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,10 +8,7 @@ charset = utf-8
88
trim_trailing_whitespace = true
99
insert_final_newline = true
1010

11-
[*.{yml,yaml}]
12-
indent_size = 2
13-
14-
[.cruft.json]
11+
[{*.{yml,yaml,toml},.cruft.json}]
1512
indent_size = 2
1613

1714
[Makefile]

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

Lines changed: 64 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -23,67 +23,72 @@ body:
2323
- type: textarea
2424
id: versions
2525
attributes:
26-
label: Version information
26+
label: Versions
2727
description: |
28-
Please paste below the output of
28+
Which version of packages.
29+
30+
Please install `session-info2`, run the following command in a notebook,
31+
click the “Copy as Markdown” button, then paste the results into the text box below.
32+
33+
```python
34+
In[1]: import session_info2; session_info2.session_info(dependencies=True)
35+
```
36+
37+
Alternatively, run this in a console:
2938
3039
```python
31-
import session_info
32-
session_info.show(html=False, dependencies=True)
40+
>>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
3341
```
42+
render: python
3443
placeholder: |
35-
-----
36-
anndata 0.8.0rc2.dev27+ge524389
37-
session_info 1.0.0
38-
-----
39-
asttokens NA
40-
awkward 1.8.0
41-
backcall 0.2.0
42-
cython_runtime NA
43-
dateutil 2.8.2
44-
debugpy 1.6.0
45-
decorator 5.1.1
46-
entrypoints 0.4
47-
executing 0.8.3
48-
h5py 3.7.0
49-
ipykernel 6.15.0
50-
jedi 0.18.1
51-
mpl_toolkits NA
52-
natsort 8.1.0
53-
numpy 1.22.4
54-
packaging 21.3
55-
pandas 1.4.2
56-
parso 0.8.3
57-
pexpect 4.8.0
58-
pickleshare 0.7.5
59-
pkg_resources NA
60-
prompt_toolkit 3.0.29
61-
psutil 5.9.1
62-
ptyprocess 0.7.0
63-
pure_eval 0.2.2
64-
pydev_ipython NA
65-
pydevconsole NA
66-
pydevd 2.8.0
67-
pydevd_file_utils NA
68-
pydevd_plugins NA
69-
pydevd_tracing NA
70-
pygments 2.12.0
71-
pytz 2022.1
72-
scipy 1.8.1
73-
setuptools 62.5.0
74-
setuptools_scm NA
75-
six 1.16.0
76-
stack_data 0.3.0
77-
tornado 6.1
78-
traitlets 5.3.0
79-
wcwidth 0.2.5
80-
zmq 23.1.0
81-
-----
82-
IPython 8.4.0
83-
jupyter_client 7.3.4
84-
jupyter_core 4.10.0
85-
-----
86-
Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
87-
Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
88-
-----
89-
Session information updated at 2022-07-07 17:55
44+
anndata 0.11.3
45+
---- ----
46+
charset-normalizer 3.4.1
47+
coverage 7.7.0
48+
psutil 7.0.0
49+
dask 2024.7.1
50+
jaraco.context 5.3.0
51+
numcodecs 0.15.1
52+
jaraco.functools 4.0.1
53+
Jinja2 3.1.6
54+
sphinxcontrib-jsmath 1.0.1
55+
sphinxcontrib-htmlhelp 2.1.0
56+
toolz 1.0.0
57+
session-info2 0.1.2
58+
PyYAML 6.0.2
59+
llvmlite 0.44.0
60+
scipy 1.15.2
61+
pandas 2.2.3
62+
sphinxcontrib-devhelp 2.0.0
63+
h5py 3.13.0
64+
tblib 3.0.0
65+
setuptools-scm 8.2.0
66+
more-itertools 10.3.0
67+
msgpack 1.1.0
68+
sparse 0.15.5
69+
wrapt 1.17.2
70+
jaraco.collections 5.1.0
71+
numba 0.61.0
72+
pyarrow 19.0.1
73+
pytz 2025.1
74+
MarkupSafe 3.0.2
75+
crc32c 2.7.1
76+
sphinxcontrib-qthelp 2.0.0
77+
sphinxcontrib-serializinghtml 2.0.0
78+
zarr 2.18.4
79+
asciitree 0.3.3
80+
six 1.17.0
81+
sphinxcontrib-applehelp 2.0.0
82+
numpy 2.1.3
83+
cloudpickle 3.1.1
84+
sphinxcontrib-bibtex 2.6.3
85+
natsort 8.4.0
86+
jaraco.text 3.12.1
87+
setuptools 76.1.0
88+
Deprecated 1.2.18
89+
packaging 24.2
90+
python-dateutil 2.9.0.post0
91+
---- ----
92+
Python 3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
93+
OS Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
94+
Updated 2025-03-18 15:47

‎.github/workflows/build.yaml‎

Lines changed: 14 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -10,20 +10,24 @@ concurrency:
1010
group: ${{ github.workflow }}-${{ github.ref }}
1111
cancel-in-progress: true
1212

13+
defaults:
14+
run:
15+
# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
16+
shell: bash -euo pipefail {0}
17+
1318
jobs:
1419
package:
1520
runs-on: ubuntu-latest
1621
steps:
17-
- uses: actions/checkout@v3
18-
- name: Set up Python 3.10
19-
uses: actions/setup-python@v4
22+
- uses: actions/checkout@v4
23+
with:
24+
filter: blob:none
25+
fetch-depth: 0
26+
- name: Install uv
27+
uses: astral-sh/setup-uv@v5
2028
with:
21-
python-version: "3.10"
22-
cache: "pip"
23-
cache-dependency-path: "**/pyproject.toml"
24-
- name: Install build dependencies
25-
run: python -m pip install --upgrade pip wheel twine build
29+
cache-dependency-glob: pyproject.toml
2630
- name: Build package
27-
run: python -m build
31+
run: uv build
2832
- name: Check package
29-
run: twine check --strict dist/*.whl
33+
run: uvx twine check --strict dist/*.whl

‎.github/workflows/release.yaml‎

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,11 @@ on:
44
release:
55
types: [published]
66

7+
defaults:
8+
run:
9+
# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
10+
shell: bash -euo pipefail {0}
11+
712
# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
813
jobs:
914
release:
@@ -19,11 +24,11 @@ jobs:
1924
with:
2025
filter: blob:none
2126
fetch-depth: 0
22-
- uses: actions/setup-python@v4
27+
- name: Install uv
28+
uses: astral-sh/setup-uv@v5
2329
with:
24-
python-version: "3.x"
25-
cache: "pip"
26-
- run: pip install build
27-
- run: python -m build
30+
cache-dependency-glob: pyproject.toml
31+
- name: Build package
32+
run: uv build
2833
- name: Publish package distributions to PyPI
2934
uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test.yaml‎

Lines changed: 29 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -4,27 +4,36 @@ on:
44
push:
55
branches: [main]
66
pull_request:
7-
branches: "*"
7+
branches: [main]
8+
schedule:
9+
- cron: "0 5 1,15 * *"
10+
11+
concurrency:
12+
group: ${{ github.workflow }}-${{ github.ref }}
13+
cancel-in-progress: true
14+
15+
defaults:
16+
run:
17+
# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
18+
shell: bash -euo pipefail {0}
19+
820

921
jobs:
1022
test:
1123
runs-on: ${{ matrix.os }}
12-
defaults:
13-
run:
14-
shell: bash -e {0} # -e to fail on error
1524

1625
strategy:
1726
fail-fast: false
1827
matrix:
1928
include:
20-
# - os: ubuntu-latest
21-
# python: "3.9"
2229
- os: ubuntu-latest
23-
python: "3.11"
24-
# - os: ubuntu-latest
25-
# python: "3.11"
26-
# pip-flags: "--pre"
27-
# name: PRE-RELEASE DEPENDENCIES
30+
python: "3.10"
31+
- os: ubuntu-latest
32+
python: "3.12"
33+
- os: ubuntu-latest
34+
python: "3.12"
35+
pip-flags: "--pre"
36+
name: PRE-RELEASE DEPENDENCIES
2837

2938
name: ${{ matrix.name }} Python ${{ matrix.python }}
3039

@@ -34,30 +43,20 @@ jobs:
3443

3544
steps:
3645
- uses: actions/checkout@v4
37-
- name: Set up Python ${{ matrix.python }}
38-
uses: actions/setup-python@v5
3946
with:
40-
python-version: ${{ matrix.python }}
41-
# cache: "pip"
42-
# cache-dependency-path: "**/pyproject.toml"
43-
44-
- name: Install test dependencies
45-
run: |
46-
python -m pip install --upgrade pip wheel
47-
- name: Install dependencies
48-
run: |
49-
python -m pip install ${{ matrix.pip-flags }} ".[dev,test]"
50-
- name: Test
47+
filter: blob:none
48+
fetch-depth: 0
49+
- name: Install uv
50+
uses: astral-sh/setup-uv@v5
51+
with:
52+
cache-dependency-glob: pyproject.toml
53+
- name: run tests using hatch
5154
env:
5255
MPLBACKEND: agg
5356
PLATFORM: ${{ matrix.os }}
5457
DISPLAY: :42
55-
run: |
56-
python -m coverage run -m pytest -v --color=yes
57-
- name: Report coverage
58-
run: |
59-
python -m coverage report
58+
run: uvx hatch test --cover --python ${{ matrix.python }}
6059
- name: Upload coverage
61-
uses: codecov/codecov-action@v3
60+
uses: codecov/codecov-action@v4
6261
with:
6362
token: ${{ secrets.CODECOV_TOKEN }}

‎.gitignore‎

Lines changed: 2 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -6,24 +6,16 @@ buck-out/
66
# Compiled files
77
.venv/
88
__pycache__/
9-
.mypy_cache/
10-
.ruff_cache/
9+
.*cache/
10+
1111

1212
# Distribution / packaging
13-
/build/
1413
/dist/
15-
/*.egg-info/
1614

1715
# Tests and coverage
18-
/.pytest_cache/
19-
/.cache/
2016
/data/
2117
/node_modules/
2218

2319
# docs
2420
/docs/generated/
2521
/docs/_build/
26-
27-
# IDEs
28-
/.idea/
29-
/.vscode/

0 commit comments

Comments
 (0)