0.1.18: DDP fix + API hardening + repo polish + relax torch pin

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Report a problem with MIDAS
+title: "[BUG] "
+labels: bug
+---
+
+## Description
+<!-- What did you expect to happen? What actually happened? -->
+
+## Minimal reproducer
+<!-- Smallest possible script + the data shape, if data isn't shareable. -->
+
+```python
+# your code here
+```
+
+## Traceback
+<!-- Full traceback, not just the last line. Use a code block. -->
+
+```
+paste here
+```
+
+## Environment
+- `scmidas` version: <!-- python -c "import scmidas; print(scmidas.__version__)" -->
+- `torch` version: <!-- python -c "import torch; print(torch.__version__)" -->
+- Python: <!-- python --version -->
+- OS: <!-- e.g. Ubuntu 22.04, macOS 14.4 -->
+- Single-GPU / multi-GPU (DDP) / CPU?
+
+## Additional context
+<!-- Anything else that might help — recent change to your data, version upgrade, etc. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Question / discussion
+    url: https://github.com/labomics/midas/discussions
+    about: For usage questions and open-ended discussion, please use Discussions instead of opening an issue.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest a new capability or improvement
+title: "[FEATURE] "
+labels: enhancement
+---
+
+## What problem are you trying to solve?
+<!-- Describe the use case, not the implementation. -->
+
+## Proposed behaviour
+<!-- What would the API / output look like from a user perspective? -->
+
+## Alternatives considered
+<!-- Workarounds you've tried, related tools, etc. -->
+
+## Additional context
+<!-- Links to relevant issues, papers, datasets. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,20 @@
+<!-- Thanks for contributing to MIDAS! -->
+
+## Summary
+<!-- 1-3 sentences. What does this PR change and why? -->
+
+## Type of change
+<!-- Mark with x where applicable. -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing API to change)
+- [ ] Documentation only
+
+## Checklist
+- [ ] `pytest tests/` passes locally.
+- [ ] For new public API or behaviour changes: docstrings updated.
+- [ ] `docs/source/release.md` updated under the next version heading.
+- [ ] For non-trivial changes: an issue exists where the design was discussed.
+
+## Related issues
+<!-- e.g. Closes #123, Refs #456 -->

.github/workflows/test.yml

@@ -8,14 +8,18 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: ${{ matrix.python-version }}
           cache: pip
 
       - name: Install torch (CPU build)

.gitignore

@@ -1,4 +1,5 @@
 **/.vscode/
+**/.claude/
 **/__pycache__/
 
 **/dataset/
@@ -15,4 +16,7 @@ to_script.sh
 temp
 auto_ver.sh
 *.yaml
-.venv*
+*.png
+*.jpg
+.venv*
+.nfs*

CHANGELOG.md

@@ -0,0 +1,9 @@
+# Changelog
+
+The full release history with detailed entries lives in
+**[`docs/source/release.md`](docs/source/release.md)** and is rendered on the
+documentation site at <https://scmidas.readthedocs.io/en/latest/release.html>.
+
+This stub exists so GitHub's repo header surfaces a "CHANGELOG" link and
+tools that scan repo roots (Insights → Community Standards, Dependabot,
+release-drafter) can find it.

CODE_OF_CONDUCT.md

@@ -0,0 +1,85 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at <omicshub@outlook.com>. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at [https://www.contributor-covenant.org/faq][FAQ]. Translations are available at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

CONTRIBUTING.md

@@ -0,0 +1,52 @@
+# Contributing to MIDAS
+
+Thanks for your interest in improving MIDAS. Bug reports, documentation fixes, and pull requests are all welcome.
+
+## Reporting bugs and requesting features
+
+Please open a [GitHub issue](https://github.com/labomics/midas/issues). For bug reports, the more of the following you can provide, the faster we can help:
+
+- A minimal script that reproduces the problem.
+- The full traceback (not just the last line).
+- `python -c "import scmidas; print(scmidas.__version__)"`, your `torch.__version__`, and the OS/Python version.
+- For DDP-related issues, the value of `STRATEGY` and `GPUS` from your demo cell.
+
+## Development setup
+
+```bash
+git clone https://github.com/labomics/midas.git
+cd midas
+conda create -n scmidas python=3.12
+conda activate scmidas
+pip install -e ".[dev]"
+```
+
+The `[dev]` extra installs `pytest`, `pytest-cov`, `ruff`, `mypy`, and `build`.
+
+## Running the test suite
+
+```bash
+pytest tests/
+```
+
+CI runs the same suite on Python 3.10, 3.11, and 3.12 — please make sure `pytest` passes locally before opening a pull request.
+
+## Pull request workflow
+
+1. Branch from `main`.
+2. Keep each PR focused on a single logical change. Multiple unrelated fixes in one PR slow down review and complicate revert.
+3. Make sure `pytest tests/` is green.
+4. For non-trivial changes (new public API, behaviour change, refactor that touches >1 module), open an issue first to discuss the design — it's much cheaper to align on direction before code than after.
+5. Update `docs/source/release.md` under the next "Unreleased" / version heading.
+6. Open the pull request against `main`. CI will run automatically; once it's green, a maintainer will review.
+
+## Coding style
+
+- Follow the existing patterns in the file you're editing rather than introducing a new style.
+- `ruff` is configured (line-length 100, target Python 3.10) and runs in CI as a non-blocking lint. Code that's already clean on `ruff check .` is appreciated.
+- New public APIs should have docstrings (NumPy or Google style — both are configured in Sphinx).
+- Avoid module-level `logging.basicConfig(...)` in library code.
+
+## Questions
+
+For questions that aren't bug reports, prefer [GitHub Discussions](https://github.com/labomics/midas/discussions) (or open an issue if Discussions isn't enabled).