Add GitHub Pages content, linting + formatting checks, and code of co…

…nduct (#3) * add github pages content and linting CI * add code of conduct * Update CODE_OF_CONDUCT.MD Co-authored-by: Gregory Way <[email protected]> * adjust readme with a link * spelling update * generalize title --------- Co-authored-by: Gregory Way <[email protected]>
WayScience · Sep 16, 2024 · 93235e7 · 93235e7
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diff --git a/.github/workflows/pre-commit-checks.yml b/.github/workflows/pre-commit-checks.yml
@@ -0,0 +1,22 @@
+---
+name: tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre_commit_checks:
+    runs-on: ubuntu-22.04
+    steps:
+      # checks out the repo
+      - uses: actions/checkout@v4
+      # setup python
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      # run pre-commit
+      - uses: pre-commit/[email protected]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,26 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+  python: python3.11
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: detect-private-key
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.1
+    hooks:
+      - id: actionlint
diff --git a/CODE_OF_CONDUCT.MD b/CODE_OF_CONDUCT.MD
@@ -0,0 +1,131 @@
+# 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, socioeconomic 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 email 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 [[email protected]](mailto:[email protected]).
+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].
+
+[faq]: https://www.contributor-covenant.org/faq
+[homepage]: https://www.contributor-covenant.org
+[mozilla coc]: https://github.com/mozilla/diversity
+[translations]: https://www.contributor-covenant.org/translations
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
diff --git a/README.md b/README.md
@@ -1,17 +1,19 @@
-# Playbooks
+# Lab Playbooks
 
 Playbooks relevant to Way Lab operations.
 
+See the GitHub Pages version of this content here: [https://wayscience.github.io/playbooks/](https://wayscience.github.io/playbooks/).
+
 Top-level playbooks have information which may be relevant to other computational labs.
 Playbooks in the `/internal` folder have information specific to the Way Lab.
 
-| Playbook           | Type                  | Description                        |
-|-------------------------|-----------------------|------------------------------------|
-| [Code Strategy](code_strategy.md)       | General | Strategy for using and writing code in a scientific setting. |
-| [Conference Playbook](conference_playbook.md) | General    | Playbook for selecting and participating in conferences. |
-| [Data Strategy](data_strategy.md)       | General  | Strategy for using and storing data; includes our 3 data perspectives. |
-| [GitHub Strategy](github_strategy.md)     | General  | Strategy for using GitHub efficiently; details our 3 types of repositories. |
-| [Calendar Playbook](internal/calendar_playbook.md)     | Internal  | Playbook for joining and using Way Lab calendar. |
-| [Computer Setup](internal/computer_setup.md)     | Internal  | Instructions for lab computer setup. |
-| [Onboarding](internal/onboarding.md)     | Internal  | Onboarding materials for the Way Lab. |
-| [Remote Access](internal/remote_access.md)    | Internal  | Instructions for remotely connecting to and using Way Lab computers. |
+| Playbook                                           | Type     | Description                                                                 |
+| -------------------------------------------------- | -------- | --------------------------------------------------------------------------- |
+| [Code Strategy](code_strategy.md)                  | General  | Strategy for using and writing code in a scientific setting.                |
+| [Conference Playbook](conference_playbook.md)      | General  | Playbook for selecting and participating in conferences.                    |
+| [Data Strategy](data_strategy.md)                  | General  | Strategy for using and storing data; includes our 3 data perspectives.      |
+| [GitHub Strategy](github_strategy.md)              | General  | Strategy for using GitHub efficiently; details our 3 types of repositories. |
+| [Calendar Playbook](internal/calendar_playbook.md) | Internal | Playbook for joining and using Way Lab calendar.                            |
+| [Computer Setup](internal/computer_setup.md)       | Internal | Instructions for lab computer setup.                                        |
+| [Onboarding](internal/onboarding.md)               | Internal | Onboarding materials for the Way Lab.                                       |
+| [Remote Access](internal/remote_access.md)         | Internal | Instructions for remotely connecting to and using Way Lab computers.        |
diff --git a/code_strategy.md b/code_strategy.md
@@ -1,5 +1,7 @@
+# Code Strategy
+
 We are biomedical data scientists who use code to answer biological hypotheses and explore biological data.
-It is therefore important to define how we use, write, and share code. 
+It is therefore important to define how we use, write, and share code.
 
 ## 1. Using code
 
@@ -38,7 +40,7 @@ Good code is readable.
 Based on the logic, variable names, and documentation, anyone (especially you!) should be able to understand what your code is doing.
 Readability also means standard formatting.
 We always lint our code, and use automatic formatting wherever possible (e.g. [python black](https://github.com/psf/black)).
-We use pre-commit hooks to ensure our code follows conventions before commiting.
+We use pre-commit hooks to ensure our code follows conventions before committing.
 
 ### 3. Code should be well organized (maintainable)
 
@@ -54,12 +56,10 @@ Waylab code should (usually) follow these conventions for readable, functional c
 Note that these conventions will change as the field of biomedical data science evolves and improves.
 
 1. Use [formatted string literals (f-strings)](https://docs.python.org/3/tutorial/inputoutput.html#tut-f-strings) to concatenate or insert information into strings.
+1. Use [pathlib](https://docs.python.org/3/library/pathlib.html) to represent file-system paths.
+1. Save intermediate files in parquet (`.parquet`) format when possible.
 
-2. Use [pathlib](https://docs.python.org/3/library/pathlib.html) to represent file-system paths.
-
-3. Save intermediate files in parquet (`.parquet`) format when possible.
-
-In general, we follow these [10 simple rules for reproducible computational research](https://doi.org/10.1371/journal.pcbi.1003285). 
+In general, we follow these [10 simple rules for reproducible computational research](https://doi.org/10.1371/journal.pcbi.1003285).
 
 ## 3. Sharing code
 
@@ -95,7 +95,6 @@ Reviewing code can be tricky.
 It is important to understand someone else's code and goals, but also to let their own style shine through their work.
 We strive for individuality, understanding, and accuracy, so if you are able to spot a bug (or the potential for one), please highlight in a concise review.
 
-
 ### Code review checklist
 
 - [ ] Do you understand the code’s intention?
@@ -121,7 +120,7 @@ We strive for individuality, understanding, and accuracy, so if you are able to
 Having someone else look at your code can be scary and intimidating!
 The Waylab PI (Greg) will review your first couple pull requests to ease you into this process. However, with the lab growing and projects expanding, lab-wide pull requests are necessary.
 Work with Greg to find a pull request buddy, who will quickly become an expert on, and a cheerleader for, your project.
-Alternatively, post your pull request in the `pull-request-review` Discord channel. 
+Alternatively, post your pull request in the `pull-request-review` Discord channel.
 
 Please make your pull requests easy to review.
 They should be concise, clearly documented, and only change a minimum number of topics (ideally, 1 core change per PR).
@@ -149,14 +148,14 @@ The methodology is as follows:
 
 1. Create a new branch from _main_ for the entire refactor
 
-2. Create a new branch from the entire refactor branch for a specific change
+1. Create a new branch from the entire refactor branch for a specific change
 
-3. File a PR from this change-specific branch into the entire refactor branch
+1. File a PR from this change-specific branch into the entire refactor branch
 
-4. Someone will review your PR and after approval…
+1. Someone will review your PR and after approval…
 
-5. Squash merge the change-specific branch into the entire refactor branch
+1. Squash merge the change-specific branch into the entire refactor branch
 
-6. Repeat 2-5 for all “chunks of change”
+1. Repeat 2-5 for all “chunks of change”
 
-7. Finally, once all the changes are introduced, file a PR from the entire refactor branch into _main_!
+1. Finally, once all the changes are introduced, file a PR from the entire refactor branch into _main_!