From f1caf68a4a9401ce28fdac20e0987f7343ce24bf Mon Sep 17 00:00:00 2001 From: Zarish Abbas <90569229+zarishabbas@users.noreply.github.com> Date: Fri, 20 Oct 2023 15:19:31 -0400 Subject: [PATCH 1/6] Initial commit --- .flake8 | 2 + .github/workflows/docs.yml | 64 +++++++++ .github/workflows/lint_action.yml | 37 +++++ .github/workflows/testing.yml | 35 +++++ .gitignore | 129 +++++++++++++++++ LICENSE | 201 +++++++++++++++++++++++++++ README.md | 118 ++++++++++++++++ automate_mkdocs.py | 222 ++++++++++++++++++++++++++++++ data/readme.txt | 1 + docs/readme.txt | 1 + docs/sources/index.md | 102 ++++++++++++++ environment.yml | 11 ++ mkdocs.yml | 28 ++++ mkgendocs.yml | 11 ++ requirements.txt | 6 + results/readme.txt | 1 + scripts/readme.txt | 1 + setup.py | 6 + src/readme.txt | 1 + tests/readme.txt | 1 + tests/test_function_to_test.py | 6 + 21 files changed, 984 insertions(+) create mode 100644 .flake8 create mode 100644 .github/workflows/docs.yml create mode 100644 .github/workflows/lint_action.yml create mode 100644 .github/workflows/testing.yml create mode 100644 .gitignore create mode 100644 LICENSE create mode 100644 README.md create mode 100644 automate_mkdocs.py create mode 100644 data/readme.txt create mode 100644 docs/readme.txt create mode 100644 docs/sources/index.md create mode 100644 environment.yml create mode 100644 mkdocs.yml create mode 100644 mkgendocs.yml create mode 100644 requirements.txt create mode 100644 results/readme.txt create mode 100644 scripts/readme.txt create mode 100644 setup.py create mode 100644 src/readme.txt create mode 100644 tests/readme.txt create mode 100644 tests/test_function_to_test.py diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..7da1f96 --- /dev/null +++ b/.flake8 @@ -0,0 +1,2 @@ +[flake8] +max-line-length = 100 diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..b21b4a5 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,64 @@ +name: Docs + +on: + # Trigger the workflow on push or pull request, + # but only for the main branch + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + build: + name: Docs + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9"] + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Autogenerate new documentation + continue-on-error: true + run: | + pip install -e . + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + pip install pyyaml + python automate_mkdocs.py + git add . + - name: Update and Build GH Pages + run: | + python -m pip install --upgrade pip + pip install mkdocs==1.2.3 + pip install mkgendocs==0.9.0 + pip install markupsafe==2.0.1 + pip install jinja2==2.11 + gendocs --config mkgendocs.yml + - name: deploy + run: | + mkdocs gh-deploy --force --clean --verbose + + - name: Commit any changes to docs + continue-on-error: true + run: | + git config --local user.name "github-actions[bot]" + git add ./docs + git commit -m "Auto-updating the docs" + + + - name: Push the changes to master + continue-on-error: true + uses: ad-m/github-push-action@master + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + branch: main + force: true + + + diff --git a/.github/workflows/lint_action.yml b/.github/workflows/lint_action.yml new file mode 100644 index 0000000..5169118 --- /dev/null +++ b/.github/workflows/lint_action.yml @@ -0,0 +1,37 @@ +name: Lint + +on: + # Trigger the workflow on push or pull request, + # but only for the main branch + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + run-linters: + name: Run linters + runs-on: ubuntu-latest + + steps: + - name: Check out Git repository + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v1 + with: + python-version: 3.9 + + - name: Install Python dependencies + run: pip install black flake8 + + - name: Run linters + uses: wearerequired/lint-action@v2 + with: + auto_fix: true + black: true + black_auto_fix: true + flake8: true + flake8_auto_fix: false diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml new file mode 100644 index 0000000..db8f299 --- /dev/null +++ b/.github/workflows/testing.yml @@ -0,0 +1,35 @@ +name: Tests + +on: + # Trigger the workflow on push or pull request, + # but only for the main branch + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + build: + name: Running Tests + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9"] + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pytest + pip install -e . + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Test with pytest + run: | + pytest + diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b6e4761 --- /dev/null +++ b/.gitignore @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..5d06618 --- /dev/null +++ b/README.md @@ -0,0 +1,118 @@ +# ALLFED-Repository-Template + +**If this is the first time you want to use this template, please go through the [Github training](https://github.com/allfed/Github-Training-Repository/blob/main/README.md) first. This will give you the neccesary background knowledge to understand what is happening here. + +## How to use this template +Use this as template when you start a new project by clicking "Use this template" in the top right. + +Then follow all the descriptions below. + +## ALLFED Python Style Guide +All code written for ALLFED should follow the [PEP 8 Style Guide for Python](https://peps.python.org/pep-0008/). Especially important are: +* Keep the code well documented +* Every function needs a docstring in this form: +``` +def count_line(f, line): + """ + Counts the number of times a line occurs. Case-sensitive. + + Arguments: + f (file): the file to scan + line (str): the line to count + + Returns: + int: the number of times the line occurs. + """ +``` +* Write [decoupled code](https://goodresearch.dev/decoupled.html), e.g. Functions should do exactly one thing and be as short as possible +* Naming conventions: + - Snake case for variables and module: variable_name, my_module.py + - Camel case for class name: MyClass + - Camel case with spaces for jupyter notebook: Analyze Brain Data.ipynb +* Delete dead code! Don't outcomment code you don't use anymore, but delete it instead. If you need to find it again, that's what we have git for. +* Use Jupyter Notebooks only for explanations and visualization. The actual programming should be happening in `.py` files. +* This repository is automatically set up with Github Actions/[Lint Action](https://github.com/marketplace/actions/lint-action) that will format your code using black and check for problems with flake8 ([without E203, W503](https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated)). If either of them fails, you will not be able to merge your files unless you fix it. If this creates problem you cannot solve contact: florian@allfed.info +* You can deactivate the branch protection that makes sure that only correct and styled code can be merged, but it is not recommended. + + +To make this easier you can use linter (auto-formatter) that change your code to be formatted in PEP 8 when you safe it. E.g. [here for Spyder](https://stackoverflow.com/questions/51463223/how-to-use-pep8-module-using-spyder) or [VS Code](https://code.visualstudio.com/docs/python/linting). + +## Testing +We want to create reliable code. This means, as much of the code needs to be automatically tested, to make sure that everything runs as intended. Therefore, every possible function should have some kind of `assert` that tests if it works. We use pytest [pytest](https://docs.pytest.org/en/7.1.x/) as our main test suit. All tests that you put in the tests folder in here are automatically run every time you push code. You can read more about testing [here](https://goodresearch.dev/testing.html). To adapt the testing.yml to your repository you just have to adapt the requirements in requirements.txt. Everything else should work on its own. You can find an example of how a test file should look like in the tests folder. Once you go the testing set up, also make sure to add the testing badge to the readme of your repository. Simply change the URL to your repository in this badge: + +![Testing](https://github.com/allfed/allfed-repository-template/actions/workflows/testing.yml/badge.svg) + + +## Documenting in small projects +Documenting your code is only one part of the documentation we want to create. Every larger repository needs: +* a readme file that explains what the repository is for and how it is organized, which should contain: + - A one-sentence description of your project + - A longer description of your project + - Installation instructions + - General orientation to the codebase and usage instructions + - Links to papers + - Links to extended docs + - License + +* a tutorial Jupyter Notebook to explain how the repository is supposed to be used + + +## Documenting in big projects +All the things for the small projects, but also: +* An automated documentation via Gitub Actions. This is already set up in this repository. Is uses the code from [this post](https://towardsdatascience.com/easily-automate-and-never-touch-your-documentation-again-a98c91ce1b95) and combines it with [this one](https://blog.elmah.io/deploying-a-mkdocs-documentation-site-with-github-actions/). It also is setup that it will only look for python files in the src folder. So, make sure that everything is in there (you can changes this behavior in the main function of `automate_mkdocs.py`). To get it running do the following + * Change the names in `mkgendocs.yml` and `mkdocs.yml` so they fit your repository + * go to Settings --> Pages + * select deploy from a branch as source + * select gh-pages as branch at root (for this option to pop up the `docs.yml` file has to have run succesfully at least once, this should happen when you push anything in your repository) + * The end result will look something [like this](https://florianjehn.github.io/Seaweed-Growth-Model/) + * The automated documentation part is still a bit wip, if you run into problems contact florian@allfed.info +* Create a [visual representation](https://goodresearch.dev/_images/pcbi.1007358.g002.PNG_L.png) of how the different files interact with each other + +## Issues +Every time you come across a problem that you do not plan to fix in the next day, please open an issue in the repository to make sure that it does not get lost. This also allows you to assign tasks to other coders on the team. For a short intro to issues, see [here](https://www.youtube.com/watch?v=TKJ4RdhyB5Y). + +## Making the repository citable +All ALLFED repositories should be citable by release. For this we use [Zenodo](https://zenodo.org/). This has to be activated by an Admin (so either Florian or Morgan). Once you have a manuscript where you need to cite the repository let them know and they will activate it. This will also create a doi badge, which should be included in the readme, like this: + +--- + + +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6865646.svg)](https://doi.org/10.5281/zenodo.6865646) + + +--- + +## ALLFED Plotting Style +All plots created for ALLFED should look and feel the same. You can activate the ALLFED style by simply starting your code with: + +`plt.style.use("https://raw.githubusercontent.com/allfed/ALLFED-matplotlib-style-sheet/main/ALLFED.mplstyle")` + +If you need to create your plots in ALLFED style, while being offline just download the file and change the path to local. + +## Project Skeleton +This repository already has the folder structure we use for repositories. Every folder has an additional readme, to tell you what needs to go in there. + +## Making the repository a pip installable Python package +For some repositories it makes sense to make them installable via pip (e.g. a model we want to share easily). In this case you can use the explanation [here](https://goodresearch.dev/setup.html). This repository already contains a setup.py that can be used for that. If you want to install it to your local environment just run `pip install -e .` while being in the folder that contains setup.py. + +## Environment +Every ALLFED project is run in its own virtual environment. Therefore, every project needs an `environment.yml` file. The one in this repository is only an example and should not be used for any actual project. To create and organize virtual environments we use [conda](https://docs.conda.io/en/latest/miniconda.html). + +## Requirements +Every ALLFED project needs a requirements file that specifies what packages are needed to run the project. You can find an example file in the repository. If you use a lot of packages you can use [pipreqg](https://allfed.github.io/Seaweed-Growth-Model/) to find them all. + +## License +ALLFED publishes its code in Open Access. For this we use the [**Apache 2.0 License**](https://www.planetcrust.com/what-does-apache-2-0-license-mean). This license allows very free use of the code, but makes sure that ALLFED cannot be sued if something goes wrong with the code. The license template in this repository needs to be adapted when a new project is created. You can include the following license badge in your readme: + +[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) + +## Gitignore +The [.gitignore file](https://git-scm.com/docs/gitignore) is the default one for Python. Make sure you change it when using another programming language. + +## Further reading/Misc +* [Best Practices for Scientific Computing](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745) +* [General course to get to know the Python skills needed to the work at ALLFED](https://github.com/florianjehn/python-for-environmental-science) +* We are using [Github Copilot](https://github.com/features/copilot) to write faster and cleaner code. If you would also like to have a license contact finance@allfed.info + +## Acknowledgment +This is strongly based on the ["Good Research Code Handbook"](https://goodresearch.dev/index.html). If something here confuses you, it makes sense to read about it there. Pretty good explanations. diff --git a/automate_mkdocs.py b/automate_mkdocs.py new file mode 100644 index 0000000..95b8bcc --- /dev/null +++ b/automate_mkdocs.py @@ -0,0 +1,222 @@ +"""Automates Python scripts formatting, linting and Mkdocs documentation.""" + +import ast +import importlib +import json +import yaml +from collections import defaultdict +from pathlib import Path +from typing import Union + + +def add_val(indices, value, data): + if not len(indices): + return + element = data + for index in indices[:-1]: + element = element[index] + element[indices[-1]] = value + + +def automate_mkdocs_from_docstring( + mkdocs_dir: Union[str, Path], mkgendocs_f: str, repo_dir: Path, match_string: str +) -> dict: + """Automates the -pages for mkgendocs package by adding all Python functions in a + directory to the mkgendocs config. + Args: + mkdocs_dir (typing.Union[str, pathlib.Path]): textual directory for + the hierarchical directory & navigation in Mkdocs + mkgendocs_f (str): The configurations file for the mkgendocs package + repo_dir (pathlib.Path): textual directory to search for Python functions in + match_string (str): the text to be matches, after which the functions will be + added in mkgendocs format + Example: + >>> + >>> automate_mkdocs_from_docstring('scripts', repo_dir=Path.cwd(), match_string='pages:') + Returns: + list: list of created markdown files and their relative paths + + """ + p = repo_dir.glob("**/*.py") + scripts = [x for x in p if x.is_file()] + + if ( + Path.cwd() != repo_dir + ): # look for mkgendocs.yml in the parent file if a subdirectory is used + repo_dir = repo_dir.parent + + functions = defaultdict(dict) + structure = fix(defaultdict)() + full_repo_dir = str(repo_dir) + "/" + for script in scripts: + + with open(script, "r") as source: + tree = ast.parse(source.read()) + funcs = {"classes": [], "functions": []} + for child in ast.iter_child_nodes(tree): + try: + if isinstance( + child, (ast.FunctionDef, ast.ClassDef, ast.AsyncFunctionDef) + ): + if child.name not in ["main"]: + + relative_path = ( + str(script) + .replace(full_repo_dir, "") + .replace("/", ".") + .replace(".py", "") + ) + module = importlib.import_module(relative_path) + f_ = getattr(module, child.name) + function = f_.__name__ + if isinstance(child, (ast.ClassDef)): + funcs["classes"].append(function) + if isinstance(child, (ast.FunctionDef, ast.AsyncFunctionDef)): + funcs["functions"].append(function) + + except Exception as e: + print("trouble on importing " + script.stem) + print("did not document " + child.name) + print(str(e)) + if not funcs["classes"]: + funcs.pop("classes") + if not funcs["functions"]: + funcs.pop("functions") + if funcs: + functions[script] = funcs + with open(f"{repo_dir}/{mkgendocs_f}", "r+") as mkgen_config: + insert_string = "" + for path, function_names in functions.items(): + relative_path = str(path).replace(full_repo_dir, "").replace(".py", "") + insert_string += ( + f' - page: "{mkdocs_dir}/{relative_path}.md"\n ' + f'source: "{relative_path}.py"\n' # functions:\n' + ) + page = f"{mkdocs_dir}/{relative_path}" + split_page = page.split("/") + split_page = [" - " + s for s in split_page] + page += f".md" + + add_val(split_page, page, structure) + for class_name, class_list in function_names.items(): + insert_string += f" {class_name}:\n" + f_string = "" + for f in class_list: + insert_f_string = f" - {f}\n" + f_string += insert_f_string + + insert_string += f_string + insert_string += "\n" + + contents = mkgen_config.readlines() + if match_string in contents[-1]: + contents.append(insert_string) + else: + + for index, line in enumerate(contents): + if match_string in line and insert_string not in contents[index + 1]: + + contents = contents[: index + 1] + contents.append(insert_string) + break + + with open(f"{repo_dir}/{mkgendocs_f}", "w") as mkgen_config: + mkgen_config.writelines(contents) + + return structure + + +def automate_nav_structure( + mkdocs_dir: Union[str, Path], + mkdocs_f: str, + repo_dir: Path, + match_string: str, + structure: dict, +) -> str: + """Automates the -pages for mkgendocs package by adding all Python + functions in a directory to the mkgendocs config. + Args: + mkdocs_dir (typing.Union[str, pathlib.Path]): textual directory for + the hierarchical directory & navigation in Mkdocs + mkgendocs_f (str): The configurations file for the mkgendocs package + repo_dir (pathlib.Path): textual directory to search for Python functions in + match_string (str): the text to be matches, after which the functions + will be added in mkgendocs format + Example: + >>> + >>> automate_mkdocs_from_docstring('scripts', repo_dir=Path.cwd(), match_string='pages:') + Returns: + str: feedback message + + """ + insert_string = yaml.safe_dump(json.loads(json.dumps(structure, indent=4))).replace( + "'", "" + ) + # print(structure) + with open(f"{repo_dir}/{mkdocs_f}", "r+") as mkgen_config: + assert mkgen_config is not None + contents = mkgen_config.readlines() + if match_string in contents[-1]: + contents.append(insert_string) + else: + + for index, line in enumerate(contents): + if match_string in line and insert_string not in contents[index + 1]: + + contents = contents[: index + 1] + contents.append(insert_string) + break + + with open(f"{repo_dir}/{mkdocs_f}", "w") as mkgen_config: + mkgen_config.writelines(contents) + + +def fix(f): + """Allows creation of arbitrary length dict item + + Args: + f (type): Description of parameter `f`. + + Returns: + type: Description of returned object. + + """ + return lambda *args, **kwargs: f(fix(f), *args, **kwargs) + + +def indent(string: str) -> int: + """Count the indentation in whitespace characters. + Args: + string (str): text with indents + Returns: + int: Number of whitespace indentations + + """ + return sum(4 if char == "\t" else 1 for char in string[: -len(string.lstrip())]) + + +def main(): + """Execute when running this script.""" + # This is the path the script will look for code to document + python_tips_dir = Path.cwd().joinpath("src") + # This is the path the script will look for mkgendocs.yml + root_dir = Path.cwd() + + structure = automate_mkdocs_from_docstring( + mkdocs_dir="modules", + mkgendocs_f="mkgendocs.yml", + repo_dir=python_tips_dir, + match_string="pages:\n", + ) + + automate_nav_structure( + mkdocs_dir="modules", + mkdocs_f="mkdocs.yml", + repo_dir=root_dir, + match_string="- Home: index.md\n", + structure=structure, + ) + + +if __name__ == "__main__": + main() diff --git a/data/readme.txt b/data/readme.txt new file mode 100644 index 0000000..1b7b100 --- /dev/null +++ b/data/readme.txt @@ -0,0 +1 @@ +data: Where you put raw data for your project. You usually won’t sync this to source control, unless you use very small, text-based datasets (< 10 MBs). diff --git a/docs/readme.txt b/docs/readme.txt new file mode 100644 index 0000000..8128cbf --- /dev/null +++ b/docs/readme.txt @@ -0,0 +1 @@ +docs: Where you put documentation, including Markdown and reStructuredText (reST). Calling it docs makes it easy to publish documentation online through Github pages. diff --git a/docs/sources/index.md b/docs/sources/index.md new file mode 100644 index 0000000..450c370 --- /dev/null +++ b/docs/sources/index.md @@ -0,0 +1,102 @@ +# ALLFED-Repository-Template +Use this as template when you start a new project by clicking "Use this template" in the top right. + + +## ALLFED Python Style Guide +All code written for ALLFED should follow the [PEP 8 Style Guide for Python](https://peps.python.org/pep-0008/). Especially important are: +* Keep the code well documented +* Every function needs a docstring in this form: +``` +def count_line(f, line): + """ + Counts the number of times a line occurs. Case-sensitive. + + Arguments: + f (file): the file to scan + line (str): the line to count + + Returns: + int: the number of times the line occurs. + """ +``` +* Write [decoupled code](https://goodresearch.dev/decoupled.html), e.g. Functions should do exactly one thing and be as short as possible +* Naming conventions: + - Snake case for variables and module: variable_name, my_module.py + - Camel case for class name: MyClass + - Camel case with spaces for jupyter notebook: Analyze Brain Data.ipynb +* Delete dead code! Don't outcomment code you don't use anymore, but delete it instead. If you need to find it again, that's what we have git for. +* Use Jupyter Notebooks only for explanations and visualization. The actual programming should be happening in `.py` files. +* This repository is automatically set up with Github Actions/[Lint Action](https://github.com/marketplace/actions/lint-action) that will format your code using black and check for problems with flake8 ([without E203, W503](https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated)). If either of them fails, you will not be able to merge your files unless you fix it. If this creates problem you cannot solve contact: florian@allfed.info +* You can deactivate the branch protection that makes sure that only correct and styled code can be merged, but it is not recommended. + + +To make this easier you can use linter (auto-formatter) that change your code to be formatted in PEP 8 when you safe it. E.g. [here for Spyder](https://stackoverflow.com/questions/51463223/how-to-use-pep8-module-using-spyder) or [VS Code](https://code.visualstudio.com/docs/python/linting). + +## Testing +We want to create reliable code. This means, as much of the code needs to be automatically tested, to make sure that everything runs as intended. Therefore, every possible function should have some kind of `assert` that tests if it works. We use pytest [pytest](https://docs.pytest.org/en/7.1.x/) as our main test suit. All tests that you put in the tests folder in here are automatically run every time you push code. You can read more about testing [here](https://goodresearch.dev/testing.html). To adapt the testing.yml to your repository you just have to adapt the requirements in requirements.txt. Everything else should work on its own. You can find an example of how a test file should look like in the tests folder. Once you go the testing set up, also make sure to add the testing badge to the readme of your repository. Simply change the URL to your repository in this badge: + +![Testing](https://github.com/allfed/allfed-repository-template/actions/workflows/testing.yml/badge.svg) + + +## Documenting in small projects +Documenting your code is only one part of the documentation we want to create. Every larger repository needs: +* a readme file that explains what the repository is for and how it is organized, which should contain: + - A one-sentence description of your project + - A longer description of your project + - Installation instructions + - General orientation to the codebase and usage instructions + - Links to papers + - Links to extended docs + - License + +* a tutorial Jupyter Notebook to explain how the repository is supposed to be used + + +## Documenting in big projects +All the things for the small projects, but also: +* An automated documentation via Gitub Actions. This is already set up in this repository. Is uses the code from [this post](https://towardsdatascience.com/easily-automate-and-never-touch-your-documentation-again-a98c91ce1b95) and combines it with [this one](https://blog.elmah.io/deploying-a-mkdocs-documentation-site-with-github-actions/). It also is setup that it will only look for python files in the src folder. So, make sure that everything is in there (you can changes this behavior in the main function of `automate_mkdocs.py`). To get it running do the following + * go to Settings --> Pages + * select deploy from a branch as source + * select gh-pages as branch at root (for this option to pop up the `docs.yml` file has to have run succesfully at least once) + * The end result will look something [like this](https://florianjehn.github.io/Seaweed-Growth-Model/) + * The automated documentation part is still a bit wip, if you run into problems contact florian@allfed.info +* Create a [visual representation](https://goodresearch.dev/_images/pcbi.1007358.g002.PNG_L.png) of how the different files interact with each other + +## Making the repository citable +All ALLFED repositories should be citable by release. For this we use [Zenodo](https://zenodo.org/). This has to be activated by an Admin (so either Florian or Morgan). Once you have a manuscript where you need to cite the repository let them know and they will activate it. This will also create a doi badge, which should be included in the readme, like this: + +--- + + +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6865646.svg)](https://doi.org/10.5281/zenodo.6865646) + + +--- + +## Project Skeleton +This repository already has the folder structure we use for repositories. Every folder has an additional readme, to tell you what needs to go in there. + +## Making the repository a pip installable Python package +For some repositories it makes sense to make them installable via pip (e.g. a model we want to share easily). In this case you can use the explanation [here](https://goodresearch.dev/setup.html). This repository already contains a setup.py that can be used for that. + +## Environment +Every ALLFED project is run in its own virtual environment. Therefore, every project needs an `environment.yml` file. The one in this repository is only an example and should not be used for any actual project. To create and organize virtual environments we use [conda](https://docs.conda.io/en/latest/miniconda.html). + +## Requirements +Every ALLFED project needs a requirements file that specifies what packages are needed to run the project. You can find an example file in the repository. If you use a lot of packages you can use [pipreqg](https://allfed.github.io/Seaweed-Growth-Model/) to find them all. + +## License +ALLFED publishes its code in Open Access. For this we use the [**Apache 2.0 License**](https://www.planetcrust.com/what-does-apache-2-0-license-mean). This license allows very free use of the code, but makes sure that ALLFED cannot be sued if something goes wrong with the code. The license template in this repository needs to be adapted when a new project is created. You can include the following license badge in your readme: + +[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) + +## Gitignore +The [.gitignore file](https://git-scm.com/docs/gitignore) is the default one for Python. Make sure you change it when using another programming language. + +## Further reading/Misc +* [Best Practices for Scientific Computing](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745) +* [General course to get to know the Python skills needed to the work at ALLFED](https://github.com/florianjehn/python-for-environmental-science) +* We are using [Github Copilot](https://github.com/features/copilot) to write faster and cleaner code. If you would also like to have a license contact finance@allfed.info + +## Acknowledgment +This is strongly based on the ["Good Research Code Handbook"](https://goodresearch.dev/index.html). If something here confuses you, it makes sense to read about it there. Pretty good explanations. diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..64d21bd --- /dev/null +++ b/environment.yml @@ -0,0 +1,11 @@ +name: cb +channels: + - conda-forge + - defaults +dependencies: + - python=3.8 + - numpy=1.21.2 + - pip + - pip: + - tqdm==4.62.3 + diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..0b58c4a --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,28 @@ +site_name: My Super Cool Respository + + +# Repository +repo_name: My Super Cool Respository +repo_url: https://github.com/allfed/My Super-Cool-Respository +edit_uri: "" +# Copyright +copyright: Me + +docs_dir: "docs/sources" + +plugins: + - search + +theme: + name: 'readthedocs' + custom_dir: 'docs' + palette: + primary: 'white' + logo: 'assets/images/logo_full.svg' + favicon: 'assets/images/favicon.svg' + features: + - navigation.tabs + - navigation.tabs.sticky + - instant +nav: + diff --git a/mkgendocs.yml b/mkgendocs.yml new file mode 100644 index 0000000..8d9a562 --- /dev/null +++ b/mkgendocs.yml @@ -0,0 +1,11 @@ +site_name: My Super Cool Respository + + +# Repository +repo_name: My Super Cool Respository +repo: https://github.com/allfed/My-Super-Cool-Respository +# Copyright +copyright: ALLFED + +#This specifies the autogeneration portion +pages: diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..4355f56 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,6 @@ +pandas>=1.4.3 +setuptools>=61.2.0 +pytest>=7.1.2 +numpy>=1.23.1 +matplotlib>=3.5.1 +mkdocs diff --git a/results/readme.txt b/results/readme.txt new file mode 100644 index 0000000..aede27e --- /dev/null +++ b/results/readme.txt @@ -0,0 +1 @@ +results: Where you put results, including checkpoints, hdf5 files, pickle files, as well as figures and tables. If these files are heavy, you won’t put these under source control. diff --git a/scripts/readme.txt b/scripts/readme.txt new file mode 100644 index 0000000..e7c528c --- /dev/null +++ b/scripts/readme.txt @@ -0,0 +1 @@ +scripts: Where you put scripts - Python and bash alike - as well as .ipynb notebooks. diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..161f66e --- /dev/null +++ b/setup.py @@ -0,0 +1,6 @@ +from setuptools import find_packages, setup + +setup( + name="src", + packages=find_packages(), +) diff --git a/src/readme.txt b/src/readme.txt new file mode 100644 index 0000000..503277b --- /dev/null +++ b/src/readme.txt @@ -0,0 +1 @@ +src: Where you put reusable Python modules for your project. This is the kind of python code that you import. diff --git a/tests/readme.txt b/tests/readme.txt new file mode 100644 index 0000000..2cbb868 --- /dev/null +++ b/tests/readme.txt @@ -0,0 +1 @@ +tests: Where you put tests for your code. diff --git a/tests/test_function_to_test.py b/tests/test_function_to_test.py new file mode 100644 index 0000000..55ecd26 --- /dev/null +++ b/tests/test_function_to_test.py @@ -0,0 +1,6 @@ +def test_some_function(): + """ + This function tests the some_function function. + It should always return true + """ + assert some_function() is True From 6f5ce0d60ad8b5433818745f275e9acc5817b699 Mon Sep 17 00:00:00 2001 From: Lint Action Date: Fri, 20 Oct 2023 19:44:58 +0000 Subject: [PATCH 2/6] Fix code style issues with Black --- automate_mkdocs.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/automate_mkdocs.py b/automate_mkdocs.py index 95b8bcc..5555004 100644 --- a/automate_mkdocs.py +++ b/automate_mkdocs.py @@ -49,7 +49,6 @@ def automate_mkdocs_from_docstring( structure = fix(defaultdict)() full_repo_dir = str(repo_dir) + "/" for script in scripts: - with open(script, "r") as source: tree = ast.parse(source.read()) funcs = {"classes": [], "functions": []} @@ -59,7 +58,6 @@ def automate_mkdocs_from_docstring( child, (ast.FunctionDef, ast.ClassDef, ast.AsyncFunctionDef) ): if child.name not in ["main"]: - relative_path = ( str(script) .replace(full_repo_dir, "") @@ -112,10 +110,8 @@ def automate_mkdocs_from_docstring( if match_string in contents[-1]: contents.append(insert_string) else: - for index, line in enumerate(contents): if match_string in line and insert_string not in contents[index + 1]: - contents = contents[: index + 1] contents.append(insert_string) break @@ -159,10 +155,8 @@ def automate_nav_structure( if match_string in contents[-1]: contents.append(insert_string) else: - for index, line in enumerate(contents): if match_string in line and insert_string not in contents[index + 1]: - contents = contents[: index + 1] contents.append(insert_string) break From c73460e2dd34931f255dfecad2ddb33916b94025 Mon Sep 17 00:00:00 2001 From: Zarish Abbas Date: Fri, 20 Oct 2023 18:24:16 -0400 Subject: [PATCH 3/6] Added docs numerical.py plotting.py Calculate Area.ipynb test_calculate_circle_area __init__.py --- scripts/Calculate Area.ipynb | 61 +++++++++++++++++++++++++++++ src/__init__.py | 0 src/numerical.py | 16 ++++++++ src/plotting.py | 33 ++++++++++++++++ tests/test_calculate_circle_area.py | 15 +++++++ tests/test_function_to_test.py | 6 --- 6 files changed, 125 insertions(+), 6 deletions(-) create mode 100644 scripts/Calculate Area.ipynb create mode 100644 src/__init__.py create mode 100644 src/numerical.py create mode 100644 src/plotting.py create mode 100644 tests/test_calculate_circle_area.py delete mode 100644 tests/test_function_to_test.py diff --git a/scripts/Calculate Area.ipynb b/scripts/Calculate Area.ipynb new file mode 100644 index 0000000..1d54859 --- /dev/null +++ b/scripts/Calculate Area.ipynb @@ -0,0 +1,61 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Make sure that you have " + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "ename": "ModuleNotFoundError", + "evalue": "No module named 'src'", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32mc:\\Users\\zaris\\OneDrive\\Documents\\GitHub\\Github-Training-Repository\\scripts\\Calculate Area.ipynb Cell 2\u001b[0m line \u001b[0;36m2\n\u001b[0;32m 1\u001b[0m \u001b[39m#import calculating area equation\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39msrc\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mnumerical\u001b[39;00m \u001b[39mimport\u001b[39;00m calculate_circle_area\n", + "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'src'" + ] + } + ], + "source": [ + "#import calculating area equation\n", + "from src.numerical import calculate_circle_area" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "env", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/numerical.py b/src/numerical.py new file mode 100644 index 0000000..4751f1d --- /dev/null +++ b/src/numerical.py @@ -0,0 +1,16 @@ +"""Module providing a function that calculate the area of a circle.""" +import math + +def calculate_circle_area(radius): + """ + Calculates the area of a circle from its radius. + + Arguments: + radius (float): The radius of the circle. + + Returns: + float: The area of the circle. + """ + + area = math.pi * radius * radius + return area diff --git a/src/plotting.py b/src/plotting.py new file mode 100644 index 0000000..b02f65c --- /dev/null +++ b/src/plotting.py @@ -0,0 +1,33 @@ +"""Function creating a scatterplot""" + +import matplotlib.pyplot as plt + +plt.style.use( + "https://raw.githubusercontent.com/allfed/ALLFED-matplotlib-style-sheet/main/ALLFED.mplstyle" + ) + +def create_scatter_plot(x_data, y_data, title="", xlabel="", ylabel=""): + """ + Create a scatter plot with the provided x and y data. + + Arguments: + x_data (list): The data for the x-axis. + y_data (list): The data for the y-axis. + title (str): The title of the plot. + xlabel (str): The label for the x-axis. + ylabel (str): The label for the y-axis. + """ + + # Create a new figure and axes + plt.figure() + + # Create the scatter plot + plt.scatter(x_data, y_data) + + # Set the title and labels + plt.title(title) + plt.xlabel(xlabel) + plt.ylabel(ylabel) + + # Show the plot + plt.show() diff --git a/tests/test_calculate_circle_area.py b/tests/test_calculate_circle_area.py new file mode 100644 index 0000000..3daa159 --- /dev/null +++ b/tests/test_calculate_circle_area.py @@ -0,0 +1,15 @@ +"""Tests to calculate_circle_area function""" + +import math +from src.numerical import calculate_circle_area + +def test_calculate_circle_area(): + """ + Test with a positive radius, typical input + Test with radius 0, edge case + """ + radius = 5 + expected_result = math.pi * radius ** 2 + + assert calculate_circle_area(radius) == expected_result + assert calculate_circle_area(0) == 0 diff --git a/tests/test_function_to_test.py b/tests/test_function_to_test.py deleted file mode 100644 index 55ecd26..0000000 --- a/tests/test_function_to_test.py +++ /dev/null @@ -1,6 +0,0 @@ -def test_some_function(): - """ - This function tests the some_function function. - It should always return true - """ - assert some_function() is True From 51f46536c4bef4b65e3f820793c2e6cdde85f079 Mon Sep 17 00:00:00 2001 From: Lint Action Date: Fri, 20 Oct 2023 22:25:01 +0000 Subject: [PATCH 4/6] Fix code style issues with Black --- src/numerical.py | 1 + src/plotting.py | 3 ++- tests/test_calculate_circle_area.py | 3 ++- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/numerical.py b/src/numerical.py index 4751f1d..f91ca00 100644 --- a/src/numerical.py +++ b/src/numerical.py @@ -1,6 +1,7 @@ """Module providing a function that calculate the area of a circle.""" import math + def calculate_circle_area(radius): """ Calculates the area of a circle from its radius. diff --git a/src/plotting.py b/src/plotting.py index b02f65c..37cc1ee 100644 --- a/src/plotting.py +++ b/src/plotting.py @@ -4,7 +4,8 @@ plt.style.use( "https://raw.githubusercontent.com/allfed/ALLFED-matplotlib-style-sheet/main/ALLFED.mplstyle" - ) +) + def create_scatter_plot(x_data, y_data, title="", xlabel="", ylabel=""): """ diff --git a/tests/test_calculate_circle_area.py b/tests/test_calculate_circle_area.py index 3daa159..777389d 100644 --- a/tests/test_calculate_circle_area.py +++ b/tests/test_calculate_circle_area.py @@ -3,13 +3,14 @@ import math from src.numerical import calculate_circle_area + def test_calculate_circle_area(): """ Test with a positive radius, typical input Test with radius 0, edge case """ radius = 5 - expected_result = math.pi * radius ** 2 + expected_result = math.pi * radius**2 assert calculate_circle_area(radius) == expected_result assert calculate_circle_area(0) == 0 From 5d290f7ef1ce7842e785f9a5c3e8efc741665e71 Mon Sep 17 00:00:00 2001 From: Zarish Abbas Date: Fri, 20 Oct 2023 18:33:39 -0400 Subject: [PATCH 5/6] Update environment.yml --- environment.yml | 137 +++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 130 insertions(+), 7 deletions(-) diff --git a/environment.yml b/environment.yml index 64d21bd..70ce4e7 100644 --- a/environment.yml +++ b/environment.yml @@ -1,11 +1,134 @@ -name: cb +name: env channels: - conda-forge - defaults dependencies: - - python=3.8 - - numpy=1.21.2 - - pip - - pip: - - tqdm==4.62.3 - + - asttokens=2.4.0=pyhd8ed1ab_0 + - backcall=0.2.0=pyh9f0ad1d_0 + - backports=1.0=pyhd8ed1ab_3 + - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 + - brotli=1.1.0=hcfcfb64_1 + - brotli-bin=1.1.0=hcfcfb64_1 + - bzip2=1.0.8=he774522_0 + - ca-certificates=2023.7.22=h56e8100_0 + - certifi=2023.7.22=pyhd8ed1ab_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - comm=0.1.4=pyhd8ed1ab_0 + - contourpy=1.1.1=py312h0d7def4_1 + - cycler=0.12.1=pyhd8ed1ab_0 + - debugpy=1.8.0=py312h53d5487_1 + - decorator=5.1.1=pyhd8ed1ab_0 + - exceptiongroup=1.1.3=pyhd8ed1ab_0 + - executing=1.2.0=pyhd8ed1ab_0 + - expat=2.5.0=hd77b12b_0 + - fonttools=4.43.1=py312he70551f_0 + - freetype=2.12.1=hdaf720e_2 + - gettext=0.21.1=h5728263_0 + - glib=2.78.0=h12be248_0 + - glib-tools=2.78.0=h12be248_0 + - gst-plugins-base=1.22.6=h001b923_2 + - gstreamer=1.22.6=hb4038d2_2 + - icu=73.2=h63175ca_0 + - importlib-metadata=6.8.0=pyha770c72_0 + - importlib_metadata=6.8.0=hd8ed1ab_0 + - intel-openmp=2023.2.0=h57928b3_50496 + - ipykernel=6.25.2=pyh60829e3_0 + - ipython=8.16.1=pyh5737063_0 + - jedi=0.19.1=pyhd8ed1ab_0 + - jupyter_client=8.4.0=pyhd8ed1ab_0 + - jupyter_core=5.4.0=py312h2e8e312_0 + - kiwisolver=1.4.5=py312h0d7def4_1 + - krb5=1.21.2=heb0366b_0 + - lcms2=2.15=h67d730c_3 + - lerc=4.0.0=h63175ca_0 + - libblas=3.9.0=19_win64_mkl + - libbrotlicommon=1.1.0=hcfcfb64_1 + - libbrotlidec=1.1.0=hcfcfb64_1 + - libbrotlienc=1.1.0=hcfcfb64_1 + - libcblas=3.9.0=19_win64_mkl + - libclang=15.0.7=default_h77d9078_3 + - libclang13=15.0.7=default_h77d9078_3 + - libdeflate=1.19=hcfcfb64_0 + - libexpat=2.5.0=h63175ca_1 + - libffi=3.4.4=hd77b12b_0 + - libglib=2.78.0=he8f3873_0 + - libhwloc=2.9.3=default_haede6df_1009 + - libiconv=1.17=h8ffe710_0 + - libjpeg-turbo=3.0.0=hcfcfb64_1 + - liblapack=3.9.0=19_win64_mkl + - libogg=1.3.4=h8ffe710_1 + - libpng=1.6.39=h19919ed_0 + - libsodium=1.0.18=h8d14728_1 + - libsqlite=3.43.2=hcfcfb64_0 + - libtiff=4.6.0=h6e2ebb7_2 + - libvorbis=1.3.7=h0e60522_0 + - libwebp-base=1.3.2=hcfcfb64_0 + - libxcb=1.15=hcd874cb_0 + - libxml2=2.11.5=hc3477c8_1 + - libzlib=1.2.13=hcfcfb64_5 + - m2w64-gcc-libgfortran=5.3.0=6 + - m2w64-gcc-libs=5.3.0=7 + - m2w64-gcc-libs-core=5.3.0=7 + - m2w64-gmp=6.1.0=2 + - m2w64-libwinpthread-git=5.0.0.4634.697f757=2 + - matplotlib=3.8.0=py312h2e8e312_2 + - matplotlib-base=3.8.0=py312h26ecaf7_2 + - matplotlib-inline=0.1.6=pyhd8ed1ab_0 + - mkl=2023.2.0=h6a75c08_50496 + - msys2-conda-epoch=20160418=1 + - munkres=1.1.4=pyh9f0ad1d_0 + - nest-asyncio=1.5.8=pyhd8ed1ab_0 + - numpy=1.26.0=py312h8753938_0 + - openjpeg=2.5.0=h3d672ee_3 + - openssl=3.1.3=hcfcfb64_0 + - packaging=23.2=pyhd8ed1ab_0 + - parso=0.8.3=pyhd8ed1ab_0 + - pcre2=10.40=h17e33f8_0 + - pickleshare=0.7.5=py_1003 + - pillow=10.1.0=py312he768995_0 + - pip=23.3=py312haa95532_0 + - platformdirs=3.11.0=pyhd8ed1ab_0 + - ply=3.11=py_1 + - prompt-toolkit=3.0.39=pyha770c72_0 + - prompt_toolkit=3.0.39=hd8ed1ab_0 + - psutil=5.9.5=py312he70551f_1 + - pthread-stubs=0.4=hcd874cb_1001 + - pthreads-win32=2.9.1=hfa6e2cd_3 + - pure_eval=0.2.2=pyhd8ed1ab_0 + - pygments=2.16.1=pyhd8ed1ab_0 + - pyparsing=3.1.1=pyhd8ed1ab_0 + - pyqt=5.15.9=py312he09f080_5 + - pyqt5-sip=12.12.2=py312h53d5487_5 + - python=3.12.0=h2628c8c_0_cpython + - python-dateutil=2.8.2=pyhd8ed1ab_0 + - python_abi=3.12=4_cp312 + - pywin32=306=py312h53d5487_2 + - pyzmq=25.1.1=py312h8139593_1 + - qt-main=5.15.8=h9e85ed6_17 + - setuptools=68.0.0=py312haa95532_0 + - sip=6.7.12=py312h53d5487_0 + - six=1.16.0=pyh6c4a22f_0 + - sqlite=3.41.2=h2bbff1b_0 + - stack_data=0.6.2=pyhd8ed1ab_0 + - tbb=2021.10.0=h91493d7_2 + - tk=8.6.13=hcfcfb64_0 + - toml=0.10.2=pyhd8ed1ab_0 + - tomli=2.0.1=pyhd8ed1ab_0 + - tornado=6.3.3=py312he70551f_1 + - traitlets=5.11.2=pyhd8ed1ab_0 + - typing-extensions=4.8.0=hd8ed1ab_0 + - typing_extensions=4.8.0=pyha770c72_0 + - tzdata=2023c=h04d1e81_0 + - ucrt=10.0.22621.0=h57928b3_0 + - vc=14.2=h21ff451_1 + - vc14_runtime=14.36.32532=hdcecf7f_17 + - vs2015_runtime=14.36.32532=h05e6639_17 + - wcwidth=0.2.8=pyhd8ed1ab_0 + - wheel=0.37.1=pyhd3eb1b0_0 + - xorg-libxau=1.0.11=hcd874cb_0 + - xorg-libxdmcp=1.1.3=hcd874cb_0 + - xz=5.4.2=h8cc25b3_0 + - zeromq=4.3.4=h0e60522_1 + - zipp=3.17.0=pyhd8ed1ab_0 + - zstd=1.5.5=h12be248_0 +prefix: C:\Users\zaris\.conda\envs\env From e09c92677b5f51899da13739663130ccdf1a3648 Mon Sep 17 00:00:00 2001 From: Zarish Abbas Date: Fri, 20 Oct 2023 18:41:09 -0400 Subject: [PATCH 6/6] Update Calculate Area.ipynb --- scripts/Calculate Area.ipynb | 32 ++++++++++++-------------------- 1 file changed, 12 insertions(+), 20 deletions(-) diff --git a/scripts/Calculate Area.ipynb b/scripts/Calculate Area.ipynb index 1d54859..4c377fa 100644 --- a/scripts/Calculate Area.ipynb +++ b/scripts/Calculate Area.ipynb @@ -1,40 +1,32 @@ { "cells": [ { - "cell_type": "markdown", + "cell_type": "code", + "execution_count": 1, "metadata": {}, + "outputs": [], "source": [ - "Make sure that you have " + "#import calculating area equation\n", + "from src.numerical import calculate_circle_area" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "metadata": {}, "outputs": [ { - "ename": "ModuleNotFoundError", - "evalue": "No module named 'src'", - "output_type": "error", - "traceback": [ - "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[1;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)", - "\u001b[1;32mc:\\Users\\zaris\\OneDrive\\Documents\\GitHub\\Github-Training-Repository\\scripts\\Calculate Area.ipynb Cell 2\u001b[0m line \u001b[0;36m2\n\u001b[0;32m 1\u001b[0m \u001b[39m#import calculating area equation\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39msrc\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mnumerical\u001b[39;00m \u001b[39mimport\u001b[39;00m calculate_circle_area\n", - "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'src'" + "name": "stdout", + "output_type": "stream", + "text": [ + "78.53981633974483\n" ] } ], "source": [ - "#import calculating area equation\n", - "from src.numerical import calculate_circle_area" + "result = calculate_circle_area(5)\n", + "print(result)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {