diff --git a/AUTHORS.txt b/AUTHORS.txt new file mode 100644 index 0000000..6d78f96 --- /dev/null +++ b/AUTHORS.txt @@ -0,0 +1 @@ +Sarah Mouffok (maintainer) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..adb932f --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,140 @@ +# Contribution Guide + +We would love for you to contribute to the experimental-protocol-fetcher project and help make it better than it is today. +As a contributor, here are the guidelines we would like you to follow: + + - [Question or Problem?](#got-a-question) + - [Issues and Bugs](#found-a-bug) + - [Feature Requests](#missing-a-feature) + - [Submissions](#submission-guidelines) + - [Development Guidelines](#development) + - [Release Procedure](#release) + +# Got a Question? + +Please do not hesitate to raise an issue on [github project page][github]. + +# Found a Bug? + +If you find a bug in the source code, you can help us by [submitting an issue](#issues) +to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#pull-requests) with a fix. + +# Missing a Feature? + +You can *request* a new feature by [submitting an issue](#issues) to our GitHub Repository. +If you would like to *implement* a new feature, please submit an issue with a proposal for your +work first, to be sure that we can use it. + +Please consider what kind of change it is: + +* For a **Major Feature**, first open an issue and outline your proposal so that it can be +discussed. This will also allow us to better coordinate our efforts, prevent duplication of work, +and help you to craft the change so that it is successfully accepted into the project. +* **Small Features** can be crafted and directly [submitted as a Pull Request](#pull-requests). + +# Submission Guidelines + +## Issues + +Before you submit an issue, please search the issue tracker, maybe an issue for your problem +already exists and the discussion might inform you of workarounds readily available. + +We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce +and confirm it. In order to reproduce bugs we will need as much information as possible, and +preferably with an example. + +## Pull Requests + +When you wish to contribute to the code base, please consider the following guidelines: + +* Make a [fork](https://guides.github.com/activities/forking/) of this repository. +* Make your changes in your fork, in a new git branch: + + ```shell + git checkout -b my-fix-branch main + ``` +* Create your patch, **including appropriate Python test cases**. + Please check the coding [conventions](#coding-conventions) for more information. +* Run the full test suite, and ensure that all tests pass. +* Commit your changes using a descriptive commit message. + + ```shell + git commit -a + ``` +* Push your branch to GitHub: + + ```shell + git push origin my-fix-branch + ``` +* In GitHub, send a Pull Request to the `main` branch of the upstream repository of the relevant component. +* If we suggest changes then: + * Make the required updates. + * Re-run the test suites to ensure tests are still passing. + * Rebase your branch and force push to your GitHub repository (this will update your Pull Request): + + ```shell + git rebase main -i + git push -f + ``` + +That’s it! Thank you for your contribution! + +### After your pull request is merged + +After your pull request is merged, you can safely delete your branch and pull the changes from +the main (upstream) repository: + +* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows: + + ```shell + git push origin --delete my-fix-branch + ``` +* Check out the main branch: + + ```shell + git checkout main -f + ``` +* Delete the local branch: + + ```shell + git branch -D my-fix-branch + ``` +* Update your main with the latest upstream version: + + ```shell + git pull --ff upstream main + ``` + +[github]: https://github.com/BlueBrain/experimental-protocol-fetcher + +# Development Environment + +Please make sure to install the project requirements, +see the [dependencies](./README.md#dependencies) section in top README. + +This section applies to both Python versions 2 and 3. + +## Setup + +It is recommended to use `virtualenv` to develop in a sandbox environment: + +``` +virtualenv venv +. venv/bin/activate +pip install -r tests/requirement_tests.txt +``` + +## Build + +Run the following command to build incrementally the project: `pip install -e .` + +## Test + +Run the following command to run the Python unit-tests: `pytest tests` + +## Coding conventions + +The code coverage of the Python unit-tests may not decrease over time. +It means that every change must go with their corresponding Python unit-tests to +validate the library behavior as well as to demonstrate the API usage. + diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..ca41e58 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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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 2024 Blue Brain Project / EPFL + + 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. \ No newline at end of file diff --git a/README.md b/README.md index fa08294..c06a890 100644 --- a/README.md +++ b/README.md @@ -1 +1,7 @@ -# experimental_protocol_fetcher +# experimental-protocol-fetcher + +Retrieval of experimental protocols for an ME-Model. +- Gets protocols used to create the M-Model (and any of its derivations) +- Gets protocols used to create the E-Model + - Including the Morphology used by the E-Model (and any of its derivation) + - Including the ExperimentalTrace-s used by the E-Model (and any of their derivations) diff --git a/experimental_protocol_fetcher/helpers.py b/experimental_protocol_fetcher/helpers.py index 2a07ae2..cacd7e3 100644 --- a/experimental_protocol_fetcher/helpers.py +++ b/experimental_protocol_fetcher/helpers.py @@ -1,3 +1,18 @@ +# This file is part of experimental-protocol-fetcher. +# Copyright 2024 Blue Brain Project / EPFL +# +# 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. + from enum import Enum from typing import Optional, Dict diff --git a/experimental_protocol_fetcher/logger.py b/experimental_protocol_fetcher/logger.py index b3d8bda..ba6bb16 100644 --- a/experimental_protocol_fetcher/logger.py +++ b/experimental_protocol_fetcher/logger.py @@ -1,3 +1,18 @@ +# This file is part of experimental-protocol-fetcher. +# Copyright 2024 Blue Brain Project / EPFL +# +# 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. + import logging import sys diff --git a/experimental_protocol_fetcher/query.py b/experimental_protocol_fetcher/query.py index 792748c..68a1549 100644 --- a/experimental_protocol_fetcher/query.py +++ b/experimental_protocol_fetcher/query.py @@ -1,3 +1,18 @@ +# This file is part of experimental-protocol-fetcher. +# Copyright 2024 Blue Brain Project / EPFL +# +# 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. + from typing import List, Optional, Dict, Callable, Tuple from kgforge.core import KnowledgeGraphForge from getpass import getpass diff --git a/experimental_protocol_fetcher/version.py b/experimental_protocol_fetcher/version.py index 318c4a4..bf2bf7b 100644 --- a/experimental_protocol_fetcher/version.py +++ b/experimental_protocol_fetcher/version.py @@ -1 +1 @@ -__version__ = '0.1.dev2+g9ec5135.d20240603' +__version__ = '0.1.dev4+g5431ce6.d20240603' diff --git a/setup.py b/setup.py index 563241a..94c1a9e 100644 --- a/setup.py +++ b/setup.py @@ -27,7 +27,7 @@ "setuptools_scm", ], install_requires=[ - "nexusforge@git+https://github.com/BlueBrain/nexus-forge", + "nexusforge", "requests" ], extras_require={ diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..8141c7f --- /dev/null +++ b/tox.ini @@ -0,0 +1,51 @@ +[base] +name = experimental_protocol_fetcher +test_deps = + pytest + +[tox] +envlist = + lint + type + py{38,39} +requires = + nexusforge@git+https://github.com/BlueBrain/nexus-forge + +indexserver = + default = https://bbpteam.epfl.ch/repository/devpi/simple + +[testenv:lint] +description = run linters +deps = + pycodestyle + pylint +commands = + pycodestyle {[base]name} + pylint -j2 {[base]name} --rcfile=tox.ini + +[testenv:type] +description = run type checks +deps = + mypy +commands = + mypy {[base]name} --config-file tox.ini --install-types + +[testenv:clean] +deps = coverage +skip_install = true +commands = coverage erase + +[pycodestyle] +max-line-length = 180 + +[pylint] +max-line-length = 180 +disable=C0115, C0114, R0903, R0913, R0912, R0914, W0212, W0511, R0902 + +[mypy] + +[mypy-kgforge.*] +ignore_missing_imports = True + +[mypy-requests.*] +ignore_missing_imports = True