pre-commit hooks

.github/CONTRIBUTING.md

@@ -1,5 +1,4 @@
-Contributing Guidelines
-=======================
+# Contributing Guidelines
 
 First off, thanks for taking the time to contribute! :clap::+1::tada:
 
@@ -8,40 +7,75 @@ First off, thanks for taking the time to contribute! :clap::+1::tada:
 [Contributing Code](#contributing-code)
 
 [How Can I Contribute?](#how-can-i-contribute)
-  * [Reporting Bugs](#reporting-bugs)
-  * [Suggesting Enhancements](#suggesting-enhancements)
-  * [Submitting pull requests](#pull-requests)
+
+- [Reporting Bugs](#reporting-bugs)
+- [Suggesting Enhancements](#suggesting-enhancements)
+- [Submitting pull requests](#pull-requests)
 
 [Style guides](#style-guides)
-  * [git commit messages](#git-commit-messages)
-  * [documentation style guide](#documentation-style-guide)
-  * [python style guide](#python-style-guide)
 
-### Contributing Code
+- [git commit messages](#git-commit-messages)
+- [documentation style guide](#documentation-style-guide)
+- [python style guide](#python-style-guide)
 
-1. Fork the KwanLab Autometa repository. You can do this [here](https://github.com/KwanLab/Autometa).
-2. <details><summary>Add the KwanLab as the upstream remote.</summary><code>
-    git remote add upstream https://github.com/KwanLab/Autometa.git</code></details>
-3. Update your local repository with the most recent updates from the Kwan Lab.
-    - <details><summary>Update your local repository.</summary><code>git pull upstream master</code></details>
-    - <details><summary>Push changes to update your remote repository.</summary><code>git push origin master</code></details>
-4. <details><summary>Check out a branch corresponding to the feature you wish to add.</summary><code>git checkout -b your-new-feature master</code></details>
-5. File an issue with the feature you plan on adding. This will open a channel of
-communication with the core developers. See [suggesting enhancements](#suggesting-enhancements) for details.
-6. Submit a pull request! To submit a pull request - see [instructions below](#pull-requests).
+### Contributing Code
 
+1. File an issue with the feature you plan on adding. This will open a channel of
+   communication with the core developers. See [suggesting enhancements](#suggesting-enhancements) for details.
+
+2. <details>
+      <summary>Fork the KwanLab Autometa repository.</summary><summary> You can do this here: https://github.com/KwanLab/Autometa</summary>
+      <summary>Clone your fork.</summary><code>git clone https://github.com/YourUserName/Autometa.git</code>
+      <summary>Then navigate to the Autometa directory.</summary><code>cd Autometa</code>
+   </details>
+
+3. <details>
+      <summary>Add the KwanLab as the upstream remote.</summary>
+      <code>git remote add upstream https://github.com/KwanLab/Autometa.git</code>
+   </details>
+
+4. <details>
+      <summary>Check out a branch respective to the contribution you plan to make.</summary>
+      <summary>Check out the <code>hotfix</code> branch from <code>master</code> if fixing a bug.</summary><code>git checkout -b hotfix master</code>
+      <summary>If adding a feature, check out a branch corresponding to the feature you wish to add from <code>dev</code>.</summary>
+      <summary> First checkout dev</summary><code>git checkout dev</code>
+      <summary>Then checkout your feature</summary><code>git checkout -b your-new-feature dev</code>
+   </details>
+
+5. <details>
+      <summary>Update your local repository with the most recent updates from the Kwan Lab.</summary>
+      <summary>Update the <code>master</code> branch if fixing a bug.</summary><code>git pull upstream master</code>
+      <summary>Otherwise update <code>your-new-feature</code> branch with <code>dev</code> and resolve any merge conflicts.</summary><code>git pull upstream dev</code>
+      <summary><b>Note: Whenver you return to the feature, make sure to pull from upstream to ensure you are working on the most up-to-date code.</b></summary>
+      <summary>Update your local repository with any changes from the Kwan Lab.</summary>
+      <code>git push origin master</code>
+      <br>
+      or
+      <br>
+      <code>git push origin dev</code>
+      <br>
+      <code>git push origin your-new-feature</code>
+   </details>
+
+6. <details>
+      <summary>Ensure pre-commit hooks are installed.</summary>
+      <code>conda install -c conda-forge pre-commit</code>
+      <br>
+      <code>pre-commit install</code>
+   </details>
+
+7. Submit a pull request! To submit a pull request - see [instructions below](#pull-requests).
 
 ## How can I contribute?
 
 ### Reporting Bugs
 
 > **Note:** If you find a **Closed** issue that seems like it is the same thing
-that you're experiencing, open a new issue and include a link to the original
-issue in the body of your new one.
+> that you're experiencing, open a new issue and include a link to the original
+> issue in the body of your new one.
 
 When submitting a bug report, please follow the bug report [template](https://github.com/KwanLab/Autometa/blob/master/.github/ISSUE_TEMPLATE/bug_report.md).
 
-
 ### Suggesting Enhancements
 
 Feature requests may be submitted by creating a new issue. When creating this issue, please follow [this template](https://github.com/KwanLab/Autometa/blob/master/.github/ISSUE_TEMPLATE/feature_request.md). After your feature request has been submitted, a maintainer will respond with a determination of whether this feature is appropriate for Autometa. If a maintainer has not responded within a reasonable time period, you can notify the Autometa team. See [notifying the team](#notifying-the-team) for details.
@@ -58,9 +92,10 @@ Please follow these steps to have your contribution considered by the maintainer
 
 1. Follow all instructions in respective [bug_fix](https://github.com/KwanLab/Autometa/blob/master/.github/PULL_REQUEST_TEMPLATE/bug_fix.md) or [feature_change](https://github.com/KwanLab/Autometa/blob/master/.github/PULL_REQUEST_TEMPLATE/feature_change.md) templates.
 2. Follow the [style guides](#style-guides).
->Note: If writing a new file, a template.py file is provided within the autometa code base to help follow the structure requested by the Autometa team.
-Please copy and rename this file before you start writing your feature.
-The template file may be found [here](https://github.com/KwanLab/Autometa/blob/dev/docs/template.py), or you may find it within your cloned repository under 'Autometa/docs/template.py'
+
+   > Note: If writing a new file, a `template.py` file is provided within the autometa code base to help follow the structure requested by the Autometa team.
+   > Please copy and rename this file before you start writing your feature.
+   > The template file may be found [here](https://github.com/KwanLab/Autometa/blob/dev/docs/template.py), or you may find it within your cloned repository under 'Autometa/docs/template.py'
 
 3. After you submit your pull request, verify that all [status checks](https://help.github.com/articles/about-status-checks/) are passing. <details><summary>What if the status checks are failing?</summary>If a status check is failing, and you believe that the failure is unrelated to your change, please leave a comment on the pull request explaining why you believe the failure is unrelated. A maintainer will re-run the status check for you. If we conclude that the failure was a false positive, then we will open an issue to track that problem with our status check suite.</details>
 
@@ -70,42 +105,43 @@ While the above must be satisfied, additional prerequisites may be present, depe
 
 ### Git Commit Messages
 
-* Use the present tense ("Add feature" not "Added feature")
-* Limit the first line to 72 characters or less
-* Reference issues and pull requests liberally after the first line
-* Consider starting the commit message with an applicable emoji:
-    * :art: `:art:` when improving the format/structure of the code
-    * :racehorse: `:racehorse:` when improving performance
-    * :memo: `:memo:` when writing docs
-    * :penguin: `:penguin:` when fixing something on Linux
-    * :apple: `:apple:` when fixing something on macOS
-    * :bug: `:bug:` when fixing a bug
-    * :fire: `:fire:` when removing code or files
-    * :green_heart: `:green_heart:` when fixing the CI build
-    * :white_check_mark: `:white_check_mark:` when adding tests
-    * :arrow_up: `:arrow_up:` when upgrading dependencies
-    * :arrow_down: `:arrow_down:` when downgrading dependencies
+- Use the present tense ("Add feature" not "Added feature")
+- Limit the first line to 72 characters or less
+- Reference issues and pull requests liberally after the first line
+- Consider starting the commit message with an applicable emoji:
+  - :art: `:art:` when improving the format/structure of the code
+  - :racehorse: `:racehorse:` when improving performance
+  - :memo: `:memo:` when writing docs
+  - :penguin: `:penguin:` when fixing something on Linux
+  - :apple: `:apple:` when fixing something on macOS
+  - :bug: `:bug:` when fixing a bug
+  - :fire: `:fire:` when removing code or files
+  - :green_heart: `:green_heart:` when fixing the CI build
+  - :white_check_mark: `:white_check_mark:` when adding tests
+  - :arrow_up: `:arrow_up:` when upgrading dependencies
+  - :arrow_down: `:arrow_down:` when downgrading dependencies
 
 ### Documentation Style Guide
 
 Documentation is hosted on reathedocs.org which uses sphinx, a python documentation generator. Therefore a common syntax for
 documenting files within the source code is required. The Autometa team follows numpy syntax to automate as much of the documentation build as possible.
 
-* Numpy documentation [style guide](https://numpydoc.readthedocs.io/en/latest/format.html)
-* Sphinx restructured text [style guide](http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#paragraphs)
+- Numpy documentation [style guide](https://numpydoc.readthedocs.io/en/latest/format.html)
+- Sphinx restructured text [style guide](http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#paragraphs)
 
 ### Python Style Guide
 
-When in doubt, you may reference:
-
-* google's python [style guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md)
-* [PEP8](https://www.python.org/dev/peps/pep-0008/)
+We have moved all development to using the [black](black.readthedocs.io) formatter and run
+[pre-commit](https://pre-commit.com/) hooks with black such that all of the fuss with formatting according to code
+specifications can be ignored! When first cloning the repository, you should first install
+pre-commit and run `pre-commit install`. This will ensure any commits you make will be
+formatted appropriately.
 
 ### Notifying the Team
 
 You may notify the Autometa team corresponding to the respective update/bug by mentioning them in a comment within your issue or pull request.
 
->Note: Please only use <code>@KwanLab/autometa</code> if you receive no response from any of the other teams below.
+> Note: Please only use <code>@KwanLab/autometa</code> if you receive no response from any of the other teams below.
 
 | Team                                   | Area of Development                       |
 | -------------------------------------- | ----------------------------------------- |

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+exclude: "^autometa/validation"
+default_language_version:
+  python: python3.7
+repos:
+  - repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0 # Use the ref you want to point at
+    hooks:
+      - id: trailing-whitespace
+      - id: check-executables-have-shebangs
+      - id: end-of-file-fixer
+      - id: debug-statements
+      - id: check-merge-conflict

.readthedocs.yaml

@@ -10,5 +10,3 @@ sphinx:
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
-
-

autometa.py

@@ -27,5 +27,5 @@
 
 from autometa.__main__ import entrypoint
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     entrypoint()

autometa/__main__.py

@@ -34,7 +34,7 @@
 from autometa.config.user import AutometaUser
 
 
-logger = logging.getLogger('autometa')
+logger = logging.getLogger("autometa")
 
 
 def init_logger(fpath=None, verbosity=0):
@@ -73,15 +73,16 @@ def init_logger(fpath=None, verbosity=0):
     }
 
     if type(verbosity) is not int:
-        raise TypeError(f'{verbosity} must be an int! {type(verbosity)}')
+        raise TypeError(f"{verbosity} must be an int! {type(verbosity)}")
     if verbosity and verbosity not in log_levels:
-        raise ValueError(f'{verbosity} not in log_levels: {log_levels}!')
+        raise ValueError(f"{verbosity} not in log_levels: {log_levels}!")
 
     level = log_levels.get(verbosity)
 
     formatter = logging.Formatter(
-        fmt='[%(asctime)s %(levelname)s] %(name)s: %(message)s',
-        datefmt='%m/%d/%Y %I:%M:%S %p')
+        fmt="[%(asctime)s %(levelname)s] %(name)s: %(message)s",
+        datefmt="%m/%d/%Y %I:%M:%S %p",
+    )
     # Construct file/stream logging handlers
     streamhandler = logging.StreamHandler()
     streamhandler.setFormatter(formatter)
@@ -95,6 +96,7 @@ def init_logger(fpath=None, verbosity=0):
     logger.setLevel(logging.DEBUG)
     return logger
 
+
 def main(args):
     """Main logic for running autometa pipeline.
 
@@ -126,6 +128,7 @@ def main(args):
         # user.process_binning()
     # user.get_pangenomes()
 
+
 def entrypoint():
     """Main entrypoint for autometa pipeline.
 
@@ -139,43 +142,57 @@ def entrypoint():
 
     """
     import argparse
+
     # import time
     cpus = mp.cpu_count()
     parser = argparse.ArgumentParser(
-        description='Main script to run the Autometa pipeline.',
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('config',
-        help='Path to your metagenome.config file',
-        nargs='*')
-    parser.add_argument('--cpus',
-        help='Num. cpus to use when updating/constructing databases',
+        description="Main script to run the Autometa pipeline.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument("config", help="Path to your metagenome.config file", nargs="*")
+    parser.add_argument(
+        "--cpus",
+        help="Num. cpus to use when updating/constructing databases",
         type=int,
-        default=cpus)
+        default=cpus,
+    )
     parser.add_argument(
-        '-v', '--verbose', dest='verbosity', action='count', default=0,
-        help='Verbosity (between 1-2 occurrences with more leading to more '
-            'verbose logging). WARN=0, INFO=1, DEBUG=2')
-    parser.add_argument('--log', help='Path to write a log file (e.g. </path/to/autometa.log>)', type=str)
-    parser.add_argument('--check-dependencies',
-        help='Check user executables and databases accessible to Autometa and exit.',
-        action='store_true')
+        "-v",
+        "--verbose",
+        dest="verbosity",
+        action="count",
+        default=0,
+        help="Verbosity (between 1-2 occurrences with more leading to more "
+        "verbose logging). WARN=0, INFO=1, DEBUG=2",
+    )
+    parser.add_argument(
+        "--log",
+        help="Path to write a log file (e.g. </path/to/autometa.log>)",
+        type=str,
+    )
+    parser.add_argument(
+        "--check-dependencies",
+        help="Check user executables and databases accessible to Autometa and exit.",
+        action="store_true",
+    )
     args = parser.parse_args()
 
     try:
         main(args)
     except KeyboardInterrupt:
-        logger.info('User cancelled run. Exiting...')
+        logger.info("User cancelled run. Exiting...")
         sys.exit(1)
     except Exception as err:
-        issue_request = '''
+        issue_request = """
 
         Please help us fix your problem!
 
         You may file an issue with us at https://github.com/KwanLab/Autometa/issues/new/choose
-        '''
+        """
         err.issue_request = issue_request
         logger.exception(err)
         logger.info(err.issue_request)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     entrypoint()