Revise docs

.bumpversion.cfg

@@ -15,7 +15,3 @@ replace = version = {new_version}
 [bumpversion:file:CITATION.cff]
 search = version: "{current_version}"
 replace = version: "{new_version}"
-
-[bumpversion:file:docs/conf.py]
-search = version = release = '{current_version}'
-replace = version = release = '{new_version}'

.pre-commit-config.yaml

@@ -1,37 +1,36 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
+      - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-docstring-first
-    -   id: check-builtin-literals
-    -   id: check-ast
-    -   id: check-merge-conflict
-    -   id: debug-statements
-    -   id: double-quote-string-fixer
-    # -   id: check-json
-    # -   id: check-added-large-files
--   repo: https://github.com/myint/docformatter
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-docstring-first
+      - id: check-builtin-literals
+      - id: check-ast
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: double-quote-string-fixer
+    #   - id: check-json
+    #   - id: check-added-large-files
+  - repo: https://github.com/stefsmeets/nbcheckorder/
+    rev: v0.2.0
+    hooks:
+      - id: nbcheckorder
+  - repo: https://github.com/myint/docformatter
     rev: v1.6.0
     hooks:
-    -   id: docformatter
--   repo: https://github.com/pre-commit/mirrors-autopep8
+      - id: docformatter
+  - repo: https://github.com/pre-commit/mirrors-autopep8
     rev: v2.0.2
     hooks:
-    -   id: autopep8
+      - id: autopep8
         args: ['--in-place', '--ignore=E501,W504']
--   repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: 'v0.0.261'
     hooks:
-    -   id: ruff
+      - id: ruff
         args: [--fix]
--   repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
-    hooks:
-    -   id: nbstripout
-        files: ".ipynb"

.readthedocs.yaml

@@ -5,12 +5,17 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
-sphinx:
-   configuration: docs/conf.py
+mkdocs:
+  configuration: mkdocs.yml
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally declare the Python requirements required to build your docs
 python:
-   version: 3.8
    install:
    - requirements: docs/requirements.txt

.zenodo.json

@@ -13,6 +13,11 @@
     {
       "affiliation": "Amsterdam Scientific Instruments",
       "name": "Erik Hogenbirk"
+    },
+    {
+      "affiliation": "Charles University",
+      "name": "Daniel Rainer",
+      "orcid": "0000-0002-3272-3161",
     }
   ],
   "keywords": [
@@ -25,6 +30,6 @@
     "data-collection",
     "automation"
   ],
-  "license": "BSD-3",
+  "license": "BSD-3-Clause",
   "upload_type": "software"
 }

CITATION.cff

@@ -24,7 +24,7 @@ authors:
 cff-version: "1.1.0"
 date-released: 2021-08-09
 doi: "10.5281/zenodo.1090388"
-license: "BSD-3"
+license: "BSD-3-Clause"
 message: "If you use this software, please cite it using these metadata."
 title: Instamatic
 version: "1.10.0"

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# 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, 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
+[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 2.0, available at
+<https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

CONTRIBUTING.md

@@ -0,0 +1,105 @@
+# Contributing guidelines
+
+Welcome! *Instamatic* is an open-source project that aims to automate the collection of electron diffraction data. If you're trying *instamatic*, your experience, questions, bugs you encountered, and suggestions for improvement are important to the success of the project.
+
+We have a [Code of Conduct](CODE_OF_CONDUCT.md), please follow it in all your interactions with the project.
+
+## Questions, feedback, bugs
+
+Use the search function to see if someone else already ran accross the same issue. Feel free to open a new [issue here](https://github.com/instamatic-dev/instamatic/issues) to ask a question, suggest improvements/new features, or report any bugs that you ran into.
+
+## Submitting changes
+
+Even better than a good bug report is a fix for the bug or the implementation of a new feature. We welcome any contributions that help improve the code.
+
+When contributing to this repository, please first discuss the change you wish to make via an [issue](https://github.com/instamatic-dev/instamatic/issues) with the owners of this repository before making a change.
+
+Contributions can come in the form of:
+
+- Bug fixes
+- New features
+- Improvement of existing code
+- Updates to the documentation
+- ... ?
+
+We use the usual GitHub pull-request flow. For more info see [GitHub's own documentation](https://help.github.com/articles/using-pull-requests/).
+
+Typically this means:
+
+1. [Forking](https://docs.github.com/articles/about-forks) the repository and/or make a [new branch](https://docs.github.com/articles/about-branches)
+2. Making your changes
+3. Make sure that the tests pass and add your own
+4. Update the documentation is updated for new features
+5. Pushing the code back to Github
+6. [Create a new Pull Request](https://help.github.com/articles/creating-a-pull-request/)
+
+One of the code owners will review your code and request changes if needed. Once your changes have been approved, your contributions will become part of *instamatic*. 🎉
+
+## Getting started with development
+
+### Setup
+
+Clone the repository into the `instamatic` directory:
+
+```console
+git clone https://github.com/instamatic-dev/instamatic
+```
+
+Install using `virtualenv`:
+
+```console
+cd instamatic
+python3 -m venv env
+source env/bin/activate
+python3 -m pip install -e .[develop]
+```
+
+Alternatively, install using Conda:
+
+```console
+cd instamatic
+conda create -n instamatic python=3.11
+conda activate instamatic
+pip install -e .[develop]
+```
+
+### Running tests
+
+instamatic uses [pytest](https://docs.pytest.org/en/latest/) to run the tests. You can run the tests for yourself using:
+
+```console
+pytest
+```
+
+To check coverage:
+
+```console
+coverage run -m pytest
+coverage report  # to output to terminal
+coverage html    # to generate html report
+```
+
+
+### Building the documentation
+
+The documentation is written in [markdown](https://www.markdownguide.org/basic-syntax/), and uses [mkdocs](https://www.mkdocs.org/) to generate the pages.
+
+To build the documentation for yourself:
+
+```console
+pip install -e .[docs]
+mkdocs serve
+```
+
+You can find the documentation source in the [docs](https://github.com/instamatic-dev/instamatic/tree/main/docs) directory.
+If you are adding new pages, make sure to update the listing in the [`mkdocs.yml`](https://github.com/instamatic-dev/instamatic/blob/main/mkdocs.yml) under the `nav` entry.
+
+### Making a release
+
+1. Make a new [release](https://github.com/instamatic-dev/instamatic/releases).
+
+2. Under 'Choose a tag', set the tag to the new version. The versioning scheme we use is [SemVer](http://semver.org/), so bump the version (*major*/*minor*/*patch*) as needed. Bumping the version is handled transparently by `bumpversion` in [this workflow](https://github.com/instamatic-dev/instamatic/blob/main/.github/workflows/publish.yaml).
+
+3. The [upload to pypi](https://pypi.org/project/instamatic) is triggered when a release is published and handled by [this workflow](https://github.com/instamatic-dev/instamatic/actions/workflows/publish.yaml).
+
+4. The [upload to zenodo](https://zenodo.org/record/5175957) is triggered when a release is published.

docs/CODE_OF_CONDUCT.md

@@ -0,0 +1 @@
+{!../CODE_OF_CONDUCT.md!}

docs/CONTRIBUTING.md

@@ -0,0 +1 @@
+{!../CONTRIBUTING.md!}