diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index ef70bf74b..b09c03cf7 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -80,7 +80,7 @@ jobs: files: dist/* upload_test_pypi: - name: Upload to Test_PyPi + name: Upload to Test_PyPI needs: [build_wheels, build_sdist] runs-on: ubuntu-latest environment: test_pypi @@ -100,7 +100,7 @@ jobs: repository_url: https://test.pypi.org/legacy/ upload_pypi: - name: Upload to PyPi + name: Upload to PyPI needs: [build_wheels, build_sdist] runs-on: ubuntu-latest environment: pypi diff --git a/README.rst b/README.rst index 09c84454d..959deb468 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,4 @@ -|Build status| |Website pypop.org| |GitHub license| |Citations| +|PyPI version fury.io| |Build status| |Website pypop.org| |GitHub license| |Citations| PyPop: Python for Population Genomics @@ -41,9 +41,7 @@ In addition, you can also cite our 2003 Pacific Symposium on Biocomputing paper: The package name for installation purposes is |pkgname| - to avoid conflicting with an unrelated package with the name ``pypop`` - already on `PyPI `__. This is a working name and - may change and is not yet the final package name until the package - is released to PyPI. + already on `PyPI `__. Quickstart Guide ================ @@ -54,7 +52,7 @@ If you already have Python and ``pip`` installed, install a test pre-releases us .. code-block:: shell - pip install pypop-genomics --extra-index-url https://test.pypi.org/simple/ + pip install pypop-genomics Otherwise, follow `these instructions `_ to install Python 3 and pip. @@ -62,8 +60,7 @@ Otherwise, follow `these instructions `_ to install P **These pre-release versions are being made available for initial testing, they are not intended to be used for production - applications or analysis, and are not yet included in the main - pypi.org index** + applications or analysis** Once |pkgname| is installed, depending on your platform, you may also need to `adjust `_ your ``PATH`` @@ -73,7 +70,7 @@ environment variable. .. code-block:: shell - pip install -U pypop-genomics --extra-index-url https://test.pypi.org/simple/ + pip install -U pypop-genomics **Uninstalling** |pkgname| @@ -190,19 +187,17 @@ Install package from PyPI Once you have both python and ``pip`` installed, you can use ``pip`` to install pre-compiled binary "wheels" of |pkgname| -pre-releases, test packages for PyPop available directly on the `Test -PyPI `__. +pre-releases, directly from `PyPI `__. .. warning:: **These pre-release versions are being made available for initial testing, they are not intended to be used for production - applications or analysis, and are not yet included in the main - pypi.org index** + applications or analysis** .. code-block:: shell - pip install pypop-genomics --extra-index-url https://test.pypi.org/simple/ + pip install pypop-genomics .. note:: @@ -220,8 +215,22 @@ flag, i.e. .. code-block:: shell - pip install -U pypop-genomics --extra-index-url https://test.pypi.org/simple/ + pip install -U pypop-genomics +**Installing from Test PyPI** + +From time to time, we may make available packages on the `Test PyPI +`__ instance, rather than the through the main +instance. The above installation and updating instructions can be +used, by appending the following: + +.. code-block:: shell + + --extra-index-url https://test.pypi.org/simple/ + +to the above ``pip`` commands. + + **Issues with installation permission** By default, ``pip`` will attempt to install the |pkgname| @@ -246,7 +255,7 @@ install`` command, i.e.: .. code-block:: shell - pip install pypop-genomics --user --extra-index-url https://test.pypi.org/simple/ + pip install pypop-genomics --user This may be necessary in certain cases where ``pip install`` doesn't install into the expected user directory. @@ -302,7 +311,7 @@ you need to explicitly provide a URL to the release page. .. code-block:: shell - pip install pypop-genomics-1.0.0a23-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl + pip install pypop_genomics-1.0.0a23-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Post-install ``PATH`` adjustments --------------------------------- @@ -379,6 +388,12 @@ PyPop is distributed under the terms of GPLv2 .. |pkgname| replace:: ``pypop-genomics`` +.. |PyPI version fury.io| image:: https://badge.fury.io/py/pypop-genomics.svg + :target: https://pypi.python.org/pypi/pypop-genomics/ + +.. |PyPI pyversions| image:: https://img.shields.io/pypi/pyversions/pypop-genomics.svg + :target: https://pypi.python.org/pypi/pypop-genomics/ + .. |GitHub release| image:: https://img.shields.io/github/release/alexlancaster/pypop.svg :target: https://github.com/alexlancaster/pypop/releases/