diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-zenodo-client.spec | 715 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 717 insertions, 0 deletions
@@ -0,0 +1 @@ +/zenodo_client-0.3.2.tar.gz diff --git a/python-zenodo-client.spec b/python-zenodo-client.spec new file mode 100644 index 0000000..f8e6db5 --- /dev/null +++ b/python-zenodo-client.spec @@ -0,0 +1,715 @@ +%global _empty_manifest_terminate_build 0 +Name: python-zenodo-client +Version: 0.3.2 +Release: 1 +Summary: A wrapper for the Zenodo API. +License: MIT +URL: https://github.com/cthoyt/zenodo-client +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/1f/b4/11b2ce34a84d8fca21a42c7961a4d4f17ca25a5d4d943bd183f4a4f4a844/zenodo_client-0.3.2.tar.gz +BuildArch: noarch + +Requires: python3-pydantic +Requires: python3-pystow +Requires: python3-requests +Requires: python3-click +Requires: python3-more-click +Requires: python3-typing-extensions +Requires: python3-sphinx +Requires: python3-sphinx-rtd-theme +Requires: python3-sphinx-click +Requires: python3-sphinx-autodoc-typehints + +%description +<!-- +<p align="center"> + <img src="docs/source/logo.png" height="150"> +</p> +--> + +<h1 align="center"> + Zenodo Client +</h1> + +<p align="center"> + <a href="https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests"> + <img alt="Tests" src="https://github.com/cthoyt/zenodo-client/workflows/Tests/badge.svg" /> + </a> + <a href="https://github.com/cthoyt/cookiecutter-python-package"> + <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI" src="https://img.shields.io/pypi/v/zenodo_client" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/zenodo_client" /> + </a> + <a href="https://github.com/cthoyt/zenodo-client/blob/main/LICENSE"> + <img alt="PyPI - License" src="https://img.shields.io/pypi/l/zenodo_client" /> + </a> + <a href='https://zenodo_client.readthedocs.io/en/latest/?badge=latest'> + <img src='https://readthedocs.org/projects/zenodo_client/badge/?version=latest' alt='Documentation Status' /> + </a> + <a href="https://zenodo.org/badge/latestdoi/343513445"> + <img src="https://zenodo.org/badge/343513445.svg" alt="DOI"> + </a> +</p> + +A wrapper for the Zenodo API. + +## 💪 Getting Started + +The first example shows how you can set some configuration then never worry about whether it's been +uploaded already or not - all baked in with [`pystow`](https://github.com/cthoyt/pystow). On the +first time this script is run, the new deposition is made, published, and the identifier is stored +with the given key in your `~/.config/zenodo.ini`. Next time it's run, the deposition will be looked +up, and the data will be uploaded. Versioning is given automatically by date, and if multiple +versions are uploaded on one day, then a dash and the revision are appended. + +```python +from zenodo_client import Creator, Metadata, ensure_zenodo + +# Define the metadata that will be used on initial upload +data = Metadata( + title='Test Upload 3', + upload_type='dataset', + description='test description', + creators=[ + Creator( + name='Hoyt, Charles Tapley', + affiliation='Harvard Medical School', + orcid='0000-0003-4423-4370', + ), + ], +) +res = ensure_zenodo( + key='test3', # this is a unique key you pick that will be used to store + # the numeric deposition ID on your local system's cache + data=data, + paths=[ + '/Users/cthoyt/Desktop/test1.png', + ], + sandbox=True, # remove this when you're ready to upload to real Zenodo +) +from pprint import pprint + +pprint(res.json()) +``` + +A real-world example can be found here: https://github.com/cthoyt/nsockg. + +The following example shows how to use the Zenodo uploader if you already know what your deposition +identifier is. + +```python +from zenodo_client import update_zenodo + +# The ID from your deposition +SANDBOX_DEP_ID = '724868' + +# Paths to local files. Good to use in combination with resources that are always +# dumped to the same place by a given script +paths = [ + # os.path.join(DATABASE_DIRECTORY, 'alts_sample.tsv') + '/Users/cthoyt/Desktop/alts_sample.tsv', +] + +# Don't forget to set the ZENODO_API_TOKEN environment variable or +# any valid way to get zenodo/api_token from PyStow. +update_zenodo(SANDBOX_DEP_ID, paths) +``` + +The following example shows how to look up the latest version of a record. + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.get_latest_record(OOH_NA_NA_RECORD) +``` + +Even further, the latest version of `names.tsv.gz` can be automatically downloaded to the +`~/.data/zenodo/<conceptrecid>/<version>/<path>` via `pystow` with: + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.download_latest(OOH_NA_NA_RECORD, 'names.tsv.gz') +``` + +A real-world example can be found [here](https://github.com/pyobo/pyobo/blob/master/src/pyobo/resource_utils.py) +where the latest build of the [Ooh Na Na](https://cthoyt.com/2020/04/18/ooh-na-na.html) nomenclature +database is automatically downloaded from Zenodo, even though the PyOBO package only hardcodes the +first deposition ID. + +### Command Line Interface + +The zenodo_client command line tool is automatically installed. It can be used from the shell with +the `--help` flag to show all subcommands: + +```shell +$ zenodo_client --help +``` + +It can be run with `zenodo_client <deposition ID> <path 1> ... <path N>` + +## ⬇️ Installation + +The most recent release can be installed from +[PyPI](https://pypi.org/project/zenodo_client/) with: + +```bash +$ pip install zenodo_client +``` + +The most recent code and data can be installed directly from GitHub with: + +```bash +$ pip install git+https://github.com/cthoyt/zenodo-client.git +``` + +To install in development mode, use the following: + +```bash +$ git clone git+https://github.com/cthoyt/zenodo-client.git +$ cd zenodo-client +$ pip install -e . +``` + +## ⚖️ License + +The code in this package is licensed under the MIT License. + +## 🙏 Contributing + +Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See +[CONTRIBUTING.rst](https://github.com/cthoyt/zenodo-client/blob/master/CONTRIBUTING.rst) for more +information on getting involved. + +## 🍪 Cookiecutter Acknowledgement + +This package was created with [@audreyr](https://github.com/audreyr)'s +[cookiecutter](https://github.com/cookiecutter/cookiecutter) package +using [@cthoyt](https://github.com/cthoyt)'s +[cookiecutter-python-package](https://github.com/cthoyt/cookiecutter-python-package) template. + +## 🛠️ Development + +The final section of the README is for if you want to get involved by making a code contribution. + +### ❓ Testing + +After cloning the repository and installing `tox` with `pip install tox`, the unit tests in +the `tests/` folder can be run reproducibly with: + +```shell +$ tox +``` + +Additionally, these tests are automatically re-run with each commit in +a [GitHub Action](https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests). + +### 📦 Making a Release + +After installing the package in development mode and installing +`tox` with `pip install tox`, the commands for making a new release are contained within +the `finish` environment in `tox.ini`. Run the following from the shell: + +```shell +$ tox -e finish +``` + +This script does the following: + +1. Uses BumpVersion to switch the version number in the `setup.cfg` and + `src/zenodo_client/version.py` to not have the `-dev` suffix +2. Packages the code in both a tar archive and a wheel +3. Uploads to PyPI using `twine`. Be sure to have a `.pypirc` file configured to avoid the need for + manual input at this step +4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. +5. Bump the version to the next patch. If you made big changes and want to bump the version by + minor, you can use `tox -e bumpversion minor` after. + + +%package -n python3-zenodo-client +Summary: A wrapper for the Zenodo API. +Provides: python-zenodo-client +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-zenodo-client +<!-- +<p align="center"> + <img src="docs/source/logo.png" height="150"> +</p> +--> + +<h1 align="center"> + Zenodo Client +</h1> + +<p align="center"> + <a href="https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests"> + <img alt="Tests" src="https://github.com/cthoyt/zenodo-client/workflows/Tests/badge.svg" /> + </a> + <a href="https://github.com/cthoyt/cookiecutter-python-package"> + <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI" src="https://img.shields.io/pypi/v/zenodo_client" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/zenodo_client" /> + </a> + <a href="https://github.com/cthoyt/zenodo-client/blob/main/LICENSE"> + <img alt="PyPI - License" src="https://img.shields.io/pypi/l/zenodo_client" /> + </a> + <a href='https://zenodo_client.readthedocs.io/en/latest/?badge=latest'> + <img src='https://readthedocs.org/projects/zenodo_client/badge/?version=latest' alt='Documentation Status' /> + </a> + <a href="https://zenodo.org/badge/latestdoi/343513445"> + <img src="https://zenodo.org/badge/343513445.svg" alt="DOI"> + </a> +</p> + +A wrapper for the Zenodo API. + +## 💪 Getting Started + +The first example shows how you can set some configuration then never worry about whether it's been +uploaded already or not - all baked in with [`pystow`](https://github.com/cthoyt/pystow). On the +first time this script is run, the new deposition is made, published, and the identifier is stored +with the given key in your `~/.config/zenodo.ini`. Next time it's run, the deposition will be looked +up, and the data will be uploaded. Versioning is given automatically by date, and if multiple +versions are uploaded on one day, then a dash and the revision are appended. + +```python +from zenodo_client import Creator, Metadata, ensure_zenodo + +# Define the metadata that will be used on initial upload +data = Metadata( + title='Test Upload 3', + upload_type='dataset', + description='test description', + creators=[ + Creator( + name='Hoyt, Charles Tapley', + affiliation='Harvard Medical School', + orcid='0000-0003-4423-4370', + ), + ], +) +res = ensure_zenodo( + key='test3', # this is a unique key you pick that will be used to store + # the numeric deposition ID on your local system's cache + data=data, + paths=[ + '/Users/cthoyt/Desktop/test1.png', + ], + sandbox=True, # remove this when you're ready to upload to real Zenodo +) +from pprint import pprint + +pprint(res.json()) +``` + +A real-world example can be found here: https://github.com/cthoyt/nsockg. + +The following example shows how to use the Zenodo uploader if you already know what your deposition +identifier is. + +```python +from zenodo_client import update_zenodo + +# The ID from your deposition +SANDBOX_DEP_ID = '724868' + +# Paths to local files. Good to use in combination with resources that are always +# dumped to the same place by a given script +paths = [ + # os.path.join(DATABASE_DIRECTORY, 'alts_sample.tsv') + '/Users/cthoyt/Desktop/alts_sample.tsv', +] + +# Don't forget to set the ZENODO_API_TOKEN environment variable or +# any valid way to get zenodo/api_token from PyStow. +update_zenodo(SANDBOX_DEP_ID, paths) +``` + +The following example shows how to look up the latest version of a record. + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.get_latest_record(OOH_NA_NA_RECORD) +``` + +Even further, the latest version of `names.tsv.gz` can be automatically downloaded to the +`~/.data/zenodo/<conceptrecid>/<version>/<path>` via `pystow` with: + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.download_latest(OOH_NA_NA_RECORD, 'names.tsv.gz') +``` + +A real-world example can be found [here](https://github.com/pyobo/pyobo/blob/master/src/pyobo/resource_utils.py) +where the latest build of the [Ooh Na Na](https://cthoyt.com/2020/04/18/ooh-na-na.html) nomenclature +database is automatically downloaded from Zenodo, even though the PyOBO package only hardcodes the +first deposition ID. + +### Command Line Interface + +The zenodo_client command line tool is automatically installed. It can be used from the shell with +the `--help` flag to show all subcommands: + +```shell +$ zenodo_client --help +``` + +It can be run with `zenodo_client <deposition ID> <path 1> ... <path N>` + +## ⬇️ Installation + +The most recent release can be installed from +[PyPI](https://pypi.org/project/zenodo_client/) with: + +```bash +$ pip install zenodo_client +``` + +The most recent code and data can be installed directly from GitHub with: + +```bash +$ pip install git+https://github.com/cthoyt/zenodo-client.git +``` + +To install in development mode, use the following: + +```bash +$ git clone git+https://github.com/cthoyt/zenodo-client.git +$ cd zenodo-client +$ pip install -e . +``` + +## ⚖️ License + +The code in this package is licensed under the MIT License. + +## 🙏 Contributing + +Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See +[CONTRIBUTING.rst](https://github.com/cthoyt/zenodo-client/blob/master/CONTRIBUTING.rst) for more +information on getting involved. + +## 🍪 Cookiecutter Acknowledgement + +This package was created with [@audreyr](https://github.com/audreyr)'s +[cookiecutter](https://github.com/cookiecutter/cookiecutter) package +using [@cthoyt](https://github.com/cthoyt)'s +[cookiecutter-python-package](https://github.com/cthoyt/cookiecutter-python-package) template. + +## 🛠️ Development + +The final section of the README is for if you want to get involved by making a code contribution. + +### ❓ Testing + +After cloning the repository and installing `tox` with `pip install tox`, the unit tests in +the `tests/` folder can be run reproducibly with: + +```shell +$ tox +``` + +Additionally, these tests are automatically re-run with each commit in +a [GitHub Action](https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests). + +### 📦 Making a Release + +After installing the package in development mode and installing +`tox` with `pip install tox`, the commands for making a new release are contained within +the `finish` environment in `tox.ini`. Run the following from the shell: + +```shell +$ tox -e finish +``` + +This script does the following: + +1. Uses BumpVersion to switch the version number in the `setup.cfg` and + `src/zenodo_client/version.py` to not have the `-dev` suffix +2. Packages the code in both a tar archive and a wheel +3. Uploads to PyPI using `twine`. Be sure to have a `.pypirc` file configured to avoid the need for + manual input at this step +4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. +5. Bump the version to the next patch. If you made big changes and want to bump the version by + minor, you can use `tox -e bumpversion minor` after. + + +%package help +Summary: Development documents and examples for zenodo-client +Provides: python3-zenodo-client-doc +%description help +<!-- +<p align="center"> + <img src="docs/source/logo.png" height="150"> +</p> +--> + +<h1 align="center"> + Zenodo Client +</h1> + +<p align="center"> + <a href="https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests"> + <img alt="Tests" src="https://github.com/cthoyt/zenodo-client/workflows/Tests/badge.svg" /> + </a> + <a href="https://github.com/cthoyt/cookiecutter-python-package"> + <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI" src="https://img.shields.io/pypi/v/zenodo_client" /> + </a> + <a href="https://pypi.org/project/zenodo_client"> + <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/zenodo_client" /> + </a> + <a href="https://github.com/cthoyt/zenodo-client/blob/main/LICENSE"> + <img alt="PyPI - License" src="https://img.shields.io/pypi/l/zenodo_client" /> + </a> + <a href='https://zenodo_client.readthedocs.io/en/latest/?badge=latest'> + <img src='https://readthedocs.org/projects/zenodo_client/badge/?version=latest' alt='Documentation Status' /> + </a> + <a href="https://zenodo.org/badge/latestdoi/343513445"> + <img src="https://zenodo.org/badge/343513445.svg" alt="DOI"> + </a> +</p> + +A wrapper for the Zenodo API. + +## 💪 Getting Started + +The first example shows how you can set some configuration then never worry about whether it's been +uploaded already or not - all baked in with [`pystow`](https://github.com/cthoyt/pystow). On the +first time this script is run, the new deposition is made, published, and the identifier is stored +with the given key in your `~/.config/zenodo.ini`. Next time it's run, the deposition will be looked +up, and the data will be uploaded. Versioning is given automatically by date, and if multiple +versions are uploaded on one day, then a dash and the revision are appended. + +```python +from zenodo_client import Creator, Metadata, ensure_zenodo + +# Define the metadata that will be used on initial upload +data = Metadata( + title='Test Upload 3', + upload_type='dataset', + description='test description', + creators=[ + Creator( + name='Hoyt, Charles Tapley', + affiliation='Harvard Medical School', + orcid='0000-0003-4423-4370', + ), + ], +) +res = ensure_zenodo( + key='test3', # this is a unique key you pick that will be used to store + # the numeric deposition ID on your local system's cache + data=data, + paths=[ + '/Users/cthoyt/Desktop/test1.png', + ], + sandbox=True, # remove this when you're ready to upload to real Zenodo +) +from pprint import pprint + +pprint(res.json()) +``` + +A real-world example can be found here: https://github.com/cthoyt/nsockg. + +The following example shows how to use the Zenodo uploader if you already know what your deposition +identifier is. + +```python +from zenodo_client import update_zenodo + +# The ID from your deposition +SANDBOX_DEP_ID = '724868' + +# Paths to local files. Good to use in combination with resources that are always +# dumped to the same place by a given script +paths = [ + # os.path.join(DATABASE_DIRECTORY, 'alts_sample.tsv') + '/Users/cthoyt/Desktop/alts_sample.tsv', +] + +# Don't forget to set the ZENODO_API_TOKEN environment variable or +# any valid way to get zenodo/api_token from PyStow. +update_zenodo(SANDBOX_DEP_ID, paths) +``` + +The following example shows how to look up the latest version of a record. + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.get_latest_record(OOH_NA_NA_RECORD) +``` + +Even further, the latest version of `names.tsv.gz` can be automatically downloaded to the +`~/.data/zenodo/<conceptrecid>/<version>/<path>` via `pystow` with: + +```python +from zenodo_client import Zenodo + +zenodo = Zenodo() +OOH_NA_NA_RECORD = '4020486' +new_record = zenodo.download_latest(OOH_NA_NA_RECORD, 'names.tsv.gz') +``` + +A real-world example can be found [here](https://github.com/pyobo/pyobo/blob/master/src/pyobo/resource_utils.py) +where the latest build of the [Ooh Na Na](https://cthoyt.com/2020/04/18/ooh-na-na.html) nomenclature +database is automatically downloaded from Zenodo, even though the PyOBO package only hardcodes the +first deposition ID. + +### Command Line Interface + +The zenodo_client command line tool is automatically installed. It can be used from the shell with +the `--help` flag to show all subcommands: + +```shell +$ zenodo_client --help +``` + +It can be run with `zenodo_client <deposition ID> <path 1> ... <path N>` + +## ⬇️ Installation + +The most recent release can be installed from +[PyPI](https://pypi.org/project/zenodo_client/) with: + +```bash +$ pip install zenodo_client +``` + +The most recent code and data can be installed directly from GitHub with: + +```bash +$ pip install git+https://github.com/cthoyt/zenodo-client.git +``` + +To install in development mode, use the following: + +```bash +$ git clone git+https://github.com/cthoyt/zenodo-client.git +$ cd zenodo-client +$ pip install -e . +``` + +## ⚖️ License + +The code in this package is licensed under the MIT License. + +## 🙏 Contributing + +Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See +[CONTRIBUTING.rst](https://github.com/cthoyt/zenodo-client/blob/master/CONTRIBUTING.rst) for more +information on getting involved. + +## 🍪 Cookiecutter Acknowledgement + +This package was created with [@audreyr](https://github.com/audreyr)'s +[cookiecutter](https://github.com/cookiecutter/cookiecutter) package +using [@cthoyt](https://github.com/cthoyt)'s +[cookiecutter-python-package](https://github.com/cthoyt/cookiecutter-python-package) template. + +## 🛠️ Development + +The final section of the README is for if you want to get involved by making a code contribution. + +### ❓ Testing + +After cloning the repository and installing `tox` with `pip install tox`, the unit tests in +the `tests/` folder can be run reproducibly with: + +```shell +$ tox +``` + +Additionally, these tests are automatically re-run with each commit in +a [GitHub Action](https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests). + +### 📦 Making a Release + +After installing the package in development mode and installing +`tox` with `pip install tox`, the commands for making a new release are contained within +the `finish` environment in `tox.ini`. Run the following from the shell: + +```shell +$ tox -e finish +``` + +This script does the following: + +1. Uses BumpVersion to switch the version number in the `setup.cfg` and + `src/zenodo_client/version.py` to not have the `-dev` suffix +2. Packages the code in both a tar archive and a wheel +3. Uploads to PyPI using `twine`. Be sure to have a `.pypirc` file configured to avoid the need for + manual input at this step +4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. +5. Bump the version to the next patch. If you made big changes and want to bump the version by + minor, you can use `tox -e bumpversion minor` after. + + +%prep +%autosetup -n zenodo-client-0.3.2 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-zenodo-client -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 0.3.2-1 +- Package Spec generated @@ -0,0 +1 @@ +65b7c03b35231df5936bf8cb7d3470f1 zenodo_client-0.3.2.tar.gz |