Skip to content

Commit e610774

Browse files
amyheatheramyheather
authored
Merge pull request #72 from pythonhealthdatascience/dev
Dev
2 parents dd64301 + 7cf8c46 commit e610774

27 files changed

+1750
-2255
lines changed

‎.github/workflows/tests.yaml‎

Lines changed: 31 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,8 @@ jobs:
3333
3434
# Run tests using matrix strategy
3535
tests:
36+
permissions:
37+
contents: write
3638
needs: setup-matrix
3739
runs-on: ${{ matrix.os }}
3840
strategy:
@@ -57,8 +59,33 @@ jobs:
5759
if: runner.os != 'Windows'
5860
run: pip install -r requirements.txt
5961

60-
- name: Run tests
61-
run: pytest
62+
- name: Run tests (with coverage for linux)
63+
run: |
64+
if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
65+
pytest --cov --cov-report=xml
66+
else
67+
pytest
68+
fi
69+
shell: bash
70+
71+
- name: Generate coverage badge (for-the-badge style)
72+
if: matrix.os == 'ubuntu-latest'
73+
run: genbadge coverage -i coverage.xml -o images/coverage-badge.svg
6274

63-
- name: List the environment variables
64-
run: env
75+
- name: Upload coverage badge
76+
if: matrix.os == 'ubuntu-latest'
77+
uses: actions/upload-artifact@v4
78+
with:
79+
name: coverage-badge
80+
path: images/coverage-badge.svg
81+
82+
- name: Commit coverage badge
83+
if: matrix.os == 'ubuntu-latest'
84+
run: |
85+
git config --local user.email "github-actions[bot]@users.noreply.github.com"
86+
git config --local user.name "github-actions[bot]"
87+
git add images/coverage-badge.svg
88+
git commit -m "ci(tests): update coverage badge" || echo "No changes to commit"
89+
git push
90+
env:
91+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎CODE_OF_CONDUCT.md‎

Lines changed: 128 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,128 @@
1+
2+
# Contributor Covenant Code of Conduct
3+
4+
## Our Pledge
5+
6+
We as members, contributors, and leaders pledge to make participation in our
7+
community a harassment-free experience for everyone, regardless of age, body
8+
size, visible or invisible disability, ethnicity, sex characteristics, gender
9+
identity and expression, level of experience, education, socio-economic status,
10+
nationality, personal appearance, race, caste, color, religion, or sexual
11+
identity and orientation.
12+
13+
We pledge to act and interact in ways that contribute to an open, welcoming,
14+
diverse, inclusive, and healthy community.
15+
16+
## Our Standards
17+
18+
Examples of behavior that contributes to a positive environment for our
19+
community include:
20+
21+
- Demonstrating empathy and kindness toward other people
22+
- Being respectful of differing opinions, viewpoints, and experiences
23+
- Giving and gracefully accepting constructive feedback
24+
- Accepting responsibility and apologizing to those affected by our mistakes,
25+
and learning from the experience
26+
- Focusing on what is best not just for us as individuals, but for the overall
27+
community
28+
29+
Examples of unacceptable behavior include:
30+
31+
- The use of sexualized language or imagery, and sexual attention or advances of
32+
any kind
33+
- Trolling, insulting or derogatory comments, and personal or political attacks
34+
- Public or private harassment
35+
- Publishing others' private information, such as a physical or email address,
36+
without their explicit permission
37+
- Other conduct which could reasonably be considered inappropriate in a
38+
professional setting
39+
40+
## Enforcement Responsibilities
41+
42+
Community leaders are responsible for clarifying and enforcing our standards of
43+
acceptable behavior and will take appropriate and fair corrective action in
44+
response to any behavior that they deem inappropriate, threatening, offensive,
45+
or harmful.
46+
47+
Community leaders have the right and responsibility to remove, edit, or reject
48+
comments, commits, code, wiki edits, issues, and other contributions that are
49+
not aligned to this Code of Conduct, and will communicate reasons for moderation
50+
decisions when appropriate.
51+
52+
## Scope
53+
54+
This Code of Conduct applies within all community spaces, and also applies when
55+
an individual is officially representing the community in public spaces.
56+
Examples of representing our community include using an official email address,
57+
posting via an official social media account, or acting as an appointed
58+
representative at an online or offline event.
59+
60+
## Enforcement
61+
62+
Instances of abusive, harassing, or otherwise unacceptable behavior may be
63+
reported to the community leaders responsible for enforcement at
64+
[INSERT CONTACT METHOD].
65+
All complaints will be reviewed and investigated promptly and fairly.
66+
67+
All community leaders are obligated to respect the privacy and security of the
68+
reporter of any incident.
69+
70+
## Enforcement Guidelines
71+
72+
Community leaders will follow these Community Impact Guidelines in determining
73+
the consequences for any action they deem in violation of this Code of Conduct:
74+
75+
### 1. Correction
76+
77+
**Community Impact**: Use of inappropriate language or other behavior deemed
78+
unprofessional or unwelcome in the community.
79+
80+
**Consequence**: A private, written warning from community leaders, providing
81+
clarity around the nature of the violation and an explanation of why the
82+
behavior was inappropriate. A public apology may be requested.
83+
84+
### 2. Warning
85+
86+
**Community Impact**: A violation through a single incident or series of
87+
actions.
88+
89+
**Consequence**: A warning with consequences for continued behavior. No
90+
interaction with the people involved, including unsolicited interaction with
91+
those enforcing the Code of Conduct, for a specified period of time. This
92+
includes avoiding interactions in community spaces as well as external channels
93+
like social media. Violating these terms may lead to a temporary or permanent
94+
ban.
95+
96+
### 3. Temporary Ban
97+
98+
**Community Impact**: A serious violation of community standards, including
99+
sustained inappropriate behavior.
100+
101+
**Consequence**: A temporary ban from any sort of interaction or public
102+
communication with the community for a specified period of time. No public or
103+
private interaction with the people involved, including unsolicited interaction
104+
with those enforcing the Code of Conduct, is allowed during this period.
105+
Violating these terms may lead to a permanent ban.
106+
107+
### 4. Permanent Ban
108+
109+
**Community Impact**: Demonstrating a pattern of violation of community
110+
standards, including sustained inappropriate behavior, harassment of an
111+
individual, or aggression toward or disparagement of classes of individuals.
112+
113+
**Consequence**: A permanent ban from any sort of public interaction within the
114+
community.
115+
116+
## Attribution
117+
118+
This Code of Conduct is adapted from the
119+
[Contributor Covenant](https://www.contributor-covenant.org/), version 2.1,
120+
available at
121+
<https://www.contributor-covenant.org/version/2/1/code_of_conduct/>.
122+
123+
Community Impact Guidelines were inspired by
124+
[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/inclusion).
125+
126+
For answers to common questions about this code of conduct, see the FAQ at
127+
<https://www.contributor-covenant.org/faq/>. Translations are available at
128+
<https://www.contributor-covenant.org/translations/>.

‎CONTRIBUTING.md‎

Lines changed: 135 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,143 @@
11
# Contributing
22

3-
🎉 Thank you for checking out our project! 🎉
3+
Thank you for your interest in contributing! 🤗
44

5-
This file contains guidelines on how to get in touch with us and potentially contribute towards this repository.
5+
This file covers:
66

7-
## Email
7+
* 🐞 Workflow for bug reports, feature requests and documentation improvements
8+
* 🚀 Workflow for code contributions (bug fixes, enhancements)
9+
* 🛠️ Development and testing
10+
* 📦 Updating the package
11+
* 🤝 Code of conduct
812

9-
You can contact the researchers on this project using the provided email addresses in `CITATION.cff`.
13+
<br>
1014

11-
## Suggesting changes
15+
## 🐞 Workflow for bug reports, feature requests and documentation improvements
1216

13-
If you spot an issue, you are welcome to raise this either by:
17+
Before opening an issue, please search [existing issues](https://github.com/pythonhealthdatascience/pydesrap_mms/issues) to avoid duplicates. If an issue exists, you can add a comment with additional details and/or upvote (👍) the issue. If there is not an existing issue, please open one and provide as much detail as possible.
1418

15-
* Using **GitHub Issues**.
16-
* **Forking** the repository, make your changes and submit a pull request for review.
19+
* **For feature requests or documentation improvements**, please describe your suggestion clearly.
20+
* **For bugs**, include:
21+
* Steps to reproduce.
22+
* Expected and actual behaviour.
23+
* Environment details (operating system, python version, dependencies).
24+
* Relevant files (e.g. problematic `.qmd` files).
25+
26+
### Handling bug reports (for maintainers):
27+
28+
* Confirm reproducibility by following the reported steps.
29+
* Label the issue appropriately (e.g. `bug`).
30+
* Request additional information if necessary.
31+
* Link related issues or pull requests.
32+
* Once resolved, close the issue with a brief summary of the fix.
33+
34+
<br>
35+
36+
## 🚀 Workflow for code contributions (bug fixes, enhancements)
37+
38+
1. Fork the repository and clone your fork.
39+
40+
2. Create a new branch for your feature or fix:
41+
42+
```{.bash}
43+
git checkout -b my-feature
44+
```
45+
46+
3. Make your changes and commit them with clear, descriptive messages using the [conventional commits standard](https://www.conventionalcommits.org/en/v1.0.0/).
47+
48+
4. Push your branch to your fork:
49+
50+
```{.bash}
51+
git push origin my-feature
52+
```
53+
54+
5. Open a pull request against the main branch. Describe your changes and reference any related issues.
55+
56+
<br>
57+
58+
## 🛠️ Development and testing
59+
60+
### Dependencies
61+
62+
Set up the Python environment using `conda` (recommended):
63+
64+
```
65+
conda env create --file environment.yaml
66+
conda activate
67+
```
68+
69+
There is also a `requirements.txt` file which can be used to set up the environment with `virtualenv`, but this won't fetch a specific version of Python - so please note the version listed in `environment.yaml`.
70+
71+
<br>
72+
73+
### Docstrings
74+
75+
We follow the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) style for docstrings.
76+
77+
<br>
78+
79+
### Tests
80+
81+
Run all tests (with coverage):
82+
83+
```{.bash}
84+
pytest --cov
85+
```
86+
87+
Run tests in parallel:
88+
89+
```{.bash}
90+
pytest -n auto
91+
```
92+
93+
Run an individual test file:
94+
95+
```{.bash}
96+
pytest tests/testfile.py
97+
```
98+
99+
Run a specific test:
100+
101+
```{.bash}
102+
pytest tests/testfile.py::testname
103+
```
104+
105+
<br>
106+
107+
### Linting
108+
109+
Lint all files:
110+
111+
```{.bash}
112+
bash lint.sh
113+
```
114+
115+
Lint a specific `.py` file:
116+
117+
```{.bash}
118+
pylint simulation/model.py
119+
```
120+
121+
Lint a specific `.ipynb` file:
122+
123+
```{.bash}
124+
nbqa pylint notebooks/analysis.ipynb
125+
```
126+
127+
<br>
128+
129+
## 📦 Updating the package
130+
131+
If you are a maintainer and need to publish a new release:
132+
133+
1. Update the `CHANGELOG.md`.
134+
135+
2. Update the version number in `simulation/__init__.py` and `CITATION.cff`, and update the date in `CITATION.cff`.
136+
137+
3. Create a release on GitHub, which will automatically archive to Zenodo.
138+
139+
<br>
140+
141+
## 🤝 Code of conduct
142+
143+
Please be respectful and considerate. See the [code of conduct](https://github.com/pythonhealthdatascience/pydesrap_mms/blob/main/CODE_OF_CONDUCT.md) for details.

‎README.md‎

Lines changed: 8 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14622466.svg)](https://doi.org/10.5281/zenodo.14622466)
88
[![Tests](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml/badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml)
99
[![Linting](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/lint.yaml/badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/lint.yaml)
10-
[![ORCID](https://img.shields.io/badge/ORCID_Amy_Heather-0000--0002--6596--3479-A6CE39?&logo=orcid&logoColor=white)](https://orcid.org/0000-0002-6596-3479)
10+
[![Coverage](https://github.com/pythonhealthdatascience/pydesrap_mms/raw/main/images/coverage-badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml)
1111
</div>
1212

1313
## Repository overview
@@ -40,7 +40,7 @@ conda env create --file environment.yaml
4040
conda activate
4141
```
4242

43-
There is also a `requirements.txt` file whcih can be used to set up the environment with `virtualenv`, but this won't fetch a specific version of Python - so please note the version listed in `environment.yaml`.
43+
There is also a `requirements.txt` file which can be used to set up the environment with `virtualenv`, but this won't fetch a specific version of Python - so please note the version listed in `environment.yaml`.
4444

4545
<br>
4646

@@ -87,29 +87,6 @@ To run one notebook from the command line (with the same settings - clearing the
8787
bash run_notebooks.sh notebooks/notebook_name.ipynb
8888
```
8989

90-
**Run tests:**
91-
92-
```{.r}
93-
pytest
94-
# Run in parallel
95-
pytest -n auto
96-
# Run a specific test
97-
pytest tests/testfile.py -k 'testname'
98-
# Run with coverage
99-
pytest --cov
100-
```
101-
102-
**Lint code:**
103-
104-
```{.r}
105-
# Lint all files
106-
bash lint.sh
107-
# Lint specific .py file
108-
pylint simulation/model.py
109-
# Lint specific .ipynb file
110-
nbqa pylint notebooks/analysis.ipynb
111-
```
112-
11390
<br>
11491

11592
## How does the model work?
@@ -221,6 +198,12 @@ Run times from our analyses (on Intel Core i7-12700H, 32GB RAM, Ubuntu 24.04.1):
221198

222199
<br>
223200

201+
## Community
202+
203+
Curious about contributing? Check out the [contributing guidelines](CONTRIBUTING.md) to learn how you can help. Every bit of help counts, and your contribution - no matter how minor - is highly valued.
204+
205+
<br>
206+
224207
## Citation
225208

226209
If you use this repository, please cite either the GitHub repository or Zenodo:

‎environment.yaml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@ dependencies:
2222
- simpy=4.1.1
2323
- pip:
2424
- distfit==1.8.6
25+
- genbadge==1.1.2
2526
- kaleido==0.2.1
2627
- sim-tools==0.9.0
2728
- -e .[dev]

0 commit comments

Comments
 (0)