Skip to content

Commit 686b4f6

Browse files
scverse-botadamgayoso
scverse-bot
and
adamgayoso
authored
Update template to v0.3.0 (#125)
* Update template to v0.3.0 * Delete .github/workflows/test.yaml.rej * Update test.yaml * Delete .pre-commit-config.yaml.rej * Update .pre-commit-config.yaml * Delete .readthedocs.yaml.rej * Update .readthedocs.yaml * Delete README.md.rej * Delete pyproject.toml.rej * Update pyproject.toml * Update .pre-commit-config.yaml * Delete docs/conf.py.rej * Delete docs/index.md.rej * Update conf.py * Update .pre-commit-config.yaml * Update pyproject.toml * Update .pre-commit-config.yaml * Update release.yaml --------- Co-authored-by: scverse-bot <None> Co-authored-by: Adam Gayoso <[email protected]>
1 parent 2b48a60 commit 686b4f6

File tree

16 files changed

+339
-436
lines changed

16 files changed

+339
-436
lines changed

‎.codecov.yaml‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,17 @@
11
# Based on pydata/xarray
22
codecov:
3-
require_ci_to_pass: no
3+
require_ci_to_pass: no
44

55
coverage:
6-
status:
7-
project:
8-
default:
9-
# Require 1% coverage, i.e., always succeed
10-
target: 1
11-
patch: false
12-
changes: false
6+
status:
7+
project:
8+
default:
9+
# Require 1% coverage, i.e., always succeed
10+
target: 1
11+
patch: false
12+
changes: false
1313

1414
comment:
15-
layout: diff, flags, files
16-
behavior: once
17-
require_base: no
15+
layout: diff, flags, files
16+
behavior: once
17+
require_base: no

‎.cruft.json‎

Lines changed: 26 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -1,23 +1,28 @@
11
{
2-
"template": "https://github.com/scverse/cookiecutter-scverse",
3-
"commit": "1929d97848fd6a62fe2916dec21d6c3de99cd0a2",
4-
"checkout": "v0.2.9",
5-
"context": {
6-
"cookiecutter": {
7-
"project_name": "scib-metrics",
8-
"package_name": "scib_metrics",
9-
"project_description": "Accelerated and Python-only scIB metrics",
10-
"author_full_name": "Adam Gayoso",
11-
"author_email": "[email protected]",
12-
"github_user": "adamgayoso",
13-
"project_repo": "https://github.com/yoseflab/scib-metrics",
14-
"license": "BSD 3-Clause License",
15-
"_copy_without_render": [
16-
".github/workflows/**.yaml",
17-
"docs/_templates/autosummary/**.rst"
18-
],
19-
"_template": "https://github.com/scverse/cookiecutter-scverse"
20-
}
21-
},
22-
"directory": null
2+
"template": "https://github.com/scverse/cookiecutter-scverse",
3+
"commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
4+
"checkout": "v0.3.0",
5+
"context": {
6+
"cookiecutter": {
7+
"project_name": "scib-metrics",
8+
"package_name": "scib_metrics",
9+
"project_description": "Accelerated and Python-only scIB metrics",
10+
"author_full_name": "Adam Gayoso",
11+
"author_email": "[email protected]",
12+
"github_user": "adamgayoso",
13+
"project_repo": "https://github.com/yoseflab/scib-metrics",
14+
"license": "BSD 3-Clause License",
15+
"_copy_without_render": [
16+
".github/workflows/**.yaml",
17+
"docs/_templates/autosummary/**.rst"
18+
],
19+
"_render_devdocs": false,
20+
"_jinja2_env_vars": {
21+
"lstrip_blocks": true,
22+
"trim_blocks": true
23+
},
24+
"_template": "https://github.com/scverse/cookiecutter-scverse"
25+
}
26+
},
27+
"directory": null
2328
}

‎.editorconfig‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,5 +8,11 @@ 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]
15+
indent_size = 2
16+
1117
[Makefile]
1218
indent_style = tab

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

Lines changed: 82 additions & 82 deletions
Original file line numberDiff line numberDiff line change
@@ -2,88 +2,88 @@ name: Bug report
22
description: Report something that is broken or incorrect
33
labels: bug
44
body:
5-
- type: markdown
6-
attributes:
7-
value: |
8-
**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
9-
detailing how to provide the necessary information for us to reproduce your bug. In brief:
10-
* Please provide exact steps how to reproduce the bug in a clean Python environment.
11-
* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
12-
* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
13-
available datasets or to share a subset of your data.
5+
- type: markdown
6+
attributes:
7+
value: |
8+
**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
9+
detailing how to provide the necessary information for us to reproduce your bug. In brief:
10+
* Please provide exact steps how to reproduce the bug in a clean Python environment.
11+
* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
12+
* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
13+
available datasets or to share a subset of your data.
1414
15-
- type: textarea
16-
id: report
17-
attributes:
18-
label: Report
19-
description: A clear and concise description of what the bug is.
20-
validations:
21-
required: true
15+
- type: textarea
16+
id: report
17+
attributes:
18+
label: Report
19+
description: A clear and concise description of what the bug is.
20+
validations:
21+
required: true
2222

23-
- type: textarea
24-
id: versions
25-
attributes:
26-
label: Version information
27-
description: |
28-
Please paste below the output of
23+
- type: textarea
24+
id: versions
25+
attributes:
26+
label: Version information
27+
description: |
28+
Please paste below the output of
2929
30-
```python
31-
import session_info
32-
session_info.show(html=False, dependencies=True)
33-
```
34-
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
30+
```python
31+
import session_info
32+
session_info.show(html=False, dependencies=True)
33+
```
34+
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

‎.github/ISSUE_TEMPLATE/config.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
blank_issues_enabled: false
22
contact_links:
3-
- name: Scverse Community Forum
4-
url: https://discourse.scverse.org/
5-
about: If you have questions about “How to do X”, please ask them here.
3+
- name: Scverse Community Forum
4+
url: https://discourse.scverse.org/
5+
about: If you have questions about “How to do X”, please ask them here.

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@ name: Feature request
22
description: Propose a new feature for scib-metrics
33
labels: enhancement
44
body:
5-
- type: textarea
6-
id: description
7-
attributes:
8-
label: Description of feature
9-
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.
10-
validations:
11-
required: true
5+
- type: textarea
6+
id: description
7+
attributes:
8+
label: Description of feature
9+
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.
10+
validations:
11+
required: true

‎.github/workflows/build.yaml‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -1,29 +1,29 @@
11
name: Check Build
22

33
on:
4-
push:
5-
branches: [main]
6-
pull_request:
7-
branches: [main]
4+
push:
5+
branches: [main]
6+
pull_request:
7+
branches: [main]
88

99
concurrency:
10-
group: ${{ github.workflow }}-${{ github.ref }}
11-
cancel-in-progress: true
10+
group: ${{ github.workflow }}-${{ github.ref }}
11+
cancel-in-progress: true
1212

1313
jobs:
14-
package:
15-
runs-on: ubuntu-latest
16-
steps:
17-
- uses: actions/checkout@v3
18-
- name: Set up Python 3.10
19-
uses: actions/setup-python@v4
20-
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
26-
- name: Build package
27-
run: python -m build
28-
- name: Check package
29-
run: twine check --strict dist/*.whl
14+
package:
15+
runs-on: ubuntu-latest
16+
steps:
17+
- uses: actions/checkout@v3
18+
- name: Set up Python 3.10
19+
uses: actions/setup-python@v4
20+
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
26+
- name: Build package
27+
run: python -m build
28+
- name: Check package
29+
run: twine check --strict dist/*.whl

0 commit comments

Comments
 (0)