' + + '' + + _("Hide Search Matches") + + "
" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/api/modules.html b/api/modules.html new file mode 100644 index 0000000..449cd11 --- /dev/null +++ b/api/modules.html @@ -0,0 +1,132 @@ + + + + + + + +
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+ rheed_learn¶
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+ rheed_learn package¶
+Submodules¶
+rheed_learn.skeleton module¶
+This is a skeleton file that can serve as a starting point for a Python
+console script. To run this script uncomment the following lines in the
+[options.entry_points] section in setup.cfg:
console_scripts =
+ fibonacci = rheed_learn.skeleton:run
+Then run pip install . (or pip install -e . for editable mode)
+which will install the command fibonacci inside your current environment.
Besides console scripts, the header (i.e. until _logger…) of this file can
+also be used as template for Python modules.
+
+Note
+This file can be renamed depending on your needs or safely removed if not needed.
+References
+ + + +-
+
- +rheed_learn.skeleton.main(args)[source]¶ +
Wrapper allowing
+fib()to be called with string arguments in a CLI fashionInstead of returning the value from
+fib(), it prints the result to the +stdoutin a nicely formatted message.-
+
- Parameters: +
args (List[str]) – command line parameters as list of strings +(for example
+["--verbose", "42"]).
+
-
+
- +rheed_learn.skeleton.parse_args(args)[source]¶ +
Parse command line parameters
+-
+
- Parameters: +
args (List[str]) – command line parameters as list of strings +(for example
+["--help"]).
+- Returns: +
command line parameters namespace
+
+- Return type: +
- + +
Module contents¶
+
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+ Contributors¶
+-
+
Yichen Guo <yig319@lehigh.edu>
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+ Contributing¶
+Welcome to RHEED-Learn contributor’s guide.
This document focuses on getting any potential contributor familiarized +with the development processes, but other kinds of contributions are also +appreciated.
+If you are new to using git or have never collaborated in a project previously, +please have a look at contribution-guide.org. Other resources are also +listed in the excellent guide created by FreeCodeCamp [1].
+Please notice, all users and contributors are expected to be open, +considerate, reasonable, and respectful. When in doubt, Python Software +Foundation’s Code of Conduct is a good reference in terms of behavior +guidelines.
+Issue Reports¶
+If you experience bugs or general issues with RHEED-Learn, please have a look
+on the issue tracker. If you don’t see anything useful there, please feel
+free to fire an issue report.
+
+Tip
+Please don’t forget to include the closed issues in your search. +Sometimes a solution was already reported, and the problem is considered +solved.
+New issue reports should include information about your programming environment +(e.g., operating system, Python version) and steps to reproduce the problem. +Please try also to simplify the reproduction steps to a very minimal example +that still illustrates the problem you are facing. By removing other factors, +you help us to identify the root cause of the issue.
+Documentation Improvements¶
+You can help improve RHEED-Learn docs by making them more readable and coherent, or
+by adding missing information and correcting mistakes.
RHEED-Learn documentation uses Sphinx as its main documentation compiler.
+This means that the docs are kept in the same repository as the project code, and
+that any documentation update is done in the same way was a code contribution.
When working on documentation changes in your local machine, you can
+compile them using tox:
tox -e docs
+and use Python’s built-in web server for a preview in your web browser
+(http://localhost:8000):
python3 -m http.server --directory 'docs/_build/html'
+Code Contributions¶
+Submit an issue¶
+Before you work on any non-trivial code contribution it’s best to first create +a report in the issue tracker to start a discussion on the subject. +This often provides additional considerations and avoids unnecessary work.
+Create an environment¶
+Before you start coding, we recommend creating an isolated virtual
+environment to avoid any problems with your installed Python packages.
+This can easily be done via either virtualenv:
virtualenv <PATH TO VENV>
+source <PATH TO VENV>/bin/activate
+or Miniconda:
+conda create -n RHEED-Learn python=3 six virtualenv pytest pytest-cov
+conda activate RHEED-Learn
+Clone the repository¶
+-
+
Create an user account on GitHub if you do not already have one.
+Fork the project repository: click on the Fork button near the top of the +page. This creates a copy of the code under your account on GitHub.
+Clone this copy to your local disk:
+++git clone git@github.com:YourLogin/RHEED-Learn.git +cd RHEED-Learn +
+You should run:
+++pip install -U pip setuptools -e . +
to be able to import the package under development in the Python REPL.
+
+Install
+pre-commit:++pip install pre-commit +pre-commit install +
+RHEED-Learncomes with a lot of hooks configured to automatically help the +developer to check the code being written.
+
Implement your changes¶
+-
+
Create a branch to hold your changes:
+++git checkout -b my-feature +
and start making changes. Never work on the main branch!
+
+Start your work on this branch. Don’t forget to add docstrings to new +functions, modules and classes, especially if they are part of public APIs.
+Add yourself to the list of contributors in
AUTHORS.rst.
+When you’re done editing, do:
+++git add <MODIFIED FILES> +git commit +
to record your changes in git.
+Please make sure to see the validation messages from
+pre-commitand fix +any eventual issues. +This should automatically use flake8/black to check/fix the code style +in a way that is compatible with the project.++Important
+Don’t forget to add unit tests and documentation in case your +contribution adds an additional feature and is not just a bugfix.
+Moreover, writing a descriptive commit message is highly recommended. +In case of doubt, you can check the commit history with:
+++git log --graph --decorate --pretty=oneline --abbrev-commit --all +
to look for recurring communication patterns.
+
+Please check that your changes don’t break any unit tests with:
+++tox +(after having installed
+toxwithpip install toxorpipx).You can also use
+toxto run several other pre-configured tasks in the +repository. Trytox -avto see a list of the available checks.
+
Submit your contribution¶
+-
+
If everything works fine, push your local branch to GitHub with:
+++git push -u origin my-feature +
+Go to the web page of your fork and click “Create pull request” +to send your changes for review.
+
+
Troubleshooting¶
+The following tips can be used when facing problems to build or test the +package:
+-
+
Make sure to fetch all the tags from the upstream repository. +The command
git describe --abbrev=0 --tagsshould return the version you +are expecting. If you are trying to run CI scripts in a fork repository, +make sure to push all the tags. +You can also try to remove all the egg files or the complete egg folder, i.e., +.eggs, as well as the*.egg-infofolders in thesrcfolder or +potentially in the root of your project.
+Sometimes
+toxmisses out when new dependencies are added, especially to +setup.cfganddocs/requirements.txt. If you find any problems with +missing dependencies when running a command withtox, try to recreate the +toxenvironment using the-rflag. For example, instead of:++tox -e docs +
Try running:
+++tox -r -e docs +
+Make sure to have a reliable
+toxinstallation that uses the correct +Python version (e.g., 3.7+). When in doubt you can run:++tox --version +# OR +which tox +
If you have trouble and are seeing weird errors upon running
+tox, you can +also try to create a dedicated virtual environment with atoxbinary +freshly installed. For example:++virtualenv .venv +source .venv/bin/activate +.venv/bin/pip install tox +.venv/bin/tox -e all +
+Pytest can drop you in an interactive session in the case an error occurs. +In order to do that you need to pass a
--pdboption (for example by +runningtox -- -k <NAME OF THE FALLING TEST> --pdb). +You can also setup breakpoints manually instead of using the--pdboption.
+
Maintainer tasks¶
+Releases¶
+If you are part of the group of maintainers and have correct user permissions
+on PyPI, the following steps can be used to release a new version for
+RHEED-Learn:
-
+
Make sure all unit tests are successful.
+Tag the current commit on the main branch with a release tag, e.g.,
v1.2.3.
+Push the new tag to the upstream repository, e.g.,
git push upstream v1.2.3
+Clean up the
distandbuildfolders withtox -e clean+(orrm -rf dist build) +to avoid confusion with old builds and Sphinx docs.
+Run
tox -e buildand check that the files indisthave +the correct version (no.dirtyor git hash) according to the git tag. +Also check the sizes of the distributions, if they are too big (e.g., > +500KB), unwanted clutter may have been accidentally included.
+Run
tox -e publish -- --repository pypiand check that everything was +uploaded to PyPI correctly.
+
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+| + |
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+ RHEED-Learn¶
+This is the documentation of RHEED-Learn.
+
+
+Note
+This is the main page of your project’s Sphinx documentation.
+It is formatted in reStructuredText. Add additional pages
+by creating rst-files in docs and adding them to the toctree below.
+Use then references in order to link them from this page, e.g.
+Contributors and Changelog.
It is also possible to refer to the documentation of other Python packages
+with the Python domain syntax. By default you can reference the
+documentation of Sphinx, Python, NumPy, SciPy, matplotlib,
+Pandas, Scikit-Learn. You can add more by extending the
+intersphinx_mapping in your Sphinx’s conf.py.
The pretty useful extension autodoc is activated by default and lets +you include documentation from docstrings. Docstrings can be written in +Google style (recommended!), NumPy style and classical style.
+Contents¶
+
+
+
+Indices and tables¶
+-
+
- +
- +
- +
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diff --git a/objects.inv b/objects.inv
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+ License¶
+The MIT License (MIT)
+Copyright (c) 2024 Yichen Guo
+Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the “Software”), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
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+ Python Module Index
+ +
+ r
+
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+ | + r | ||
| + |
+ rheed_learn | + |
| + |
+ rheed_learn.skeleton | + |
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+RHEED-Learn¶
+++Add a short description here!
+
A longer description of your project goes here…
+Note¶
+This project has been set up using PyScaffold 4.6. For details and usage +information on PyScaffold see https://pyscaffold.org/.
+
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+Search.setIndex({"alltitles": {"Changelog": [[3, null]], "Clone the repository": [[4, "clone-the-repository"]], "Code Contributions": [[4, "code-contributions"]], "Contents": [[5, "contents"]], "Contributing": [[4, "contributing"]], "Contributors": [[2, null]], "Create an environment": [[4, "create-an-environment"]], "Documentation Improvements": [[4, "documentation-improvements"]], "Implement your changes": [[4, "implement-your-changes"]], "Indices and tables": [[5, "indices-and-tables"]], "Issue Reports": [[4, "issue-reports"]], "License": [[6, null]], "Maintainer tasks": [[4, "maintainer-tasks"]], "Module contents": [[1, "module-rheed_learn"]], "Note": [[7, "note"]], "RHEED-Learn": [[5, null], [7, null]], "Releases": [[4, "releases"]], "Submit an issue": [[4, "submit-an-issue"]], "Submit your contribution": [[4, "submit-your-contribution"]], "Submodules": [[1, "submodules"]], "Todo": [[4, null], [4, "id2"], [4, "id3"], [4, "id5"], [4, "id6"], [4, "id7"], [4, "id8"], [4, "id9"], [4, "id10"], [4, "id11"], [4, "id12"]], "Troubleshooting": [[4, "troubleshooting"]], "Version 0.1": [[3, "version-0-1"]], "rheed_learn": [[0, null]], "rheed_learn package": [[1, null]], "rheed_learn.skeleton module": [[1, "module-rheed_learn.skeleton"]]}, "docnames": ["api/modules", "api/rheed_learn", "authors", "changelog", "contributing", "index", "license", "readme"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api/modules.rst", "api/rheed_learn.rst", "authors.rst", "changelog.rst", "contributing.rst", "index.rst", "license.rst", "readme.rst"], "indexentries": {"fib() (in module rheed_learn.skeleton)": [[1, "rheed_learn.skeleton.fib", false]], 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