Merge remote-tracking branch 'origin/main' into replace_pval_extensio…

…n_with_scipyl

.github/release-drafter.yml

@@ -1,9 +1,10 @@
-name-template: 'PyPop 1.0.0rc3'
-tag-template: 'v1.0.0-rc3'
-prerelease: true
+name-template: 'PyPop $NEXT_PATCH_VERSION'
+tag-template: 'v$NEXT_PATCH_VERSION'
+#prerelease: true
 include-pre-releases: true
-prerelease-identifier: 'rc'
+#prerelease-identifier: 'rc'
 #version-template: '$COMPLETE'
+commitish: 'main'
 categories:
   - title: 'Features'
     labels:
@@ -37,7 +38,7 @@ version-resolver:
       - 'patch'
   default: patch
 template: |
-  ## Installation via PyPI
+  ## Install via PyPI
   ```
   pip install -U pypop-genomics
   ```
@@ -47,3 +48,5 @@ template: |
   A full history of changes is available in [`NEWS.rst`](https://github.com/alexlancaster/pypop/blob/main/NEWS.rst).
   
   $CHANGES
+
+  **Full Changelog:** https://github.com/alexlancaster/pypop/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION

.github/workflows/build_wheels.yml

@@ -13,6 +13,7 @@ on:
       - '.github/release-drafter.yml'
       - '.github/ISSUE_TEMPLATE/**'
       - '.github/workflows/documentation.yaml'
+      - '.github/workflows/buildjet_arm64.yml'
       - '.github/workflows/release-drafter.yml'
       - '.gitattributes'
   push:
@@ -26,6 +27,7 @@ on:
       - '.github/release-drafter.yml'
       - '.github/ISSUE_TEMPLATE/**'
       - '.github/workflows/documentation.yaml'
+      - '.github/workflows/buildjet_arm64.yml'      
       - '.github/workflows/release-drafter.yml'
       - '.gitattributes'
   release:

.zenodo.json

@@ -168,13 +168,13 @@
     },
     {
       "scheme": "url",
-      "identifier": "https://github.com/alexlancaster/pypop/",
+      "identifier": "https://github.com/alexlancaster/pypop/tree/v1.0.0",
       "relation": "isDerivedFrom",
       "resource_type": "software"
     },
     {
       "scheme": "url",
-      "identifier": "https://pypi.org/project/pypop-genomics/",
+      "identifier": "https://pypi.org/project/pypop-genomics/1.0.0",
       "relation": "isSourceOf",
       "resource_type": "software"
     },
@@ -207,5 +207,5 @@
   ],
   "title": "PyPop: Python for Population Genomics",
   "upload_type": "software",
-  "version": "v1.0.0-b8"
+  "version": "v1.0.0"
 }

CITATION.cff

@@ -84,5 +84,5 @@ keywords:
   - HLA
   - MHC
 license: GPL-2.0-or-later
-version: v1.0.0-rc1
-doi: 
+version: v1.0.0
+doi: 10.5281/zenodo.10080668

NEWS.rst

@@ -3,9 +3,9 @@ PyPop Release History
 
 .. _news-start:
 
-Release Notes for PyPop 1.0.0rc2
---------------------------------
-(2023-11-04)
+Release Notes for PyPop 1.0.0
+-----------------------------
+(2023-11-07)
 
 PyPop 1.0.0 is the first official release of PyPop using Python 3, and
 the first release to be included on `PyPI

README.rst

@@ -56,20 +56,14 @@ Quickstart Guide
 
 **Installing** |pkgname|
 
-If you already have Python and ``pip`` installed, install a test pre-releases using the following:
+If you already have Python and ``pip`` installed, install using the following:
 
 .. code-block:: shell
 
    pip install pypop-genomics
 
 Otherwise, follow `these instructions <Install Python 3 and pip_>`_ to install Python 3 and pip.
 
-.. warning::
-
-   **These pre-release versions are being made available for initial
-   testing, they are not intended to be used for production
-   applications or analysis**
-
 Once |pkgname| is installed, depending on your platform, you may also
 need to `adjust <Post-install PATH adjustments_>`_ your ``PATH``
 environment variable.  
@@ -113,7 +107,8 @@ well, you should see something like:
 
 .. code-block:: text
 
-   pypop 1.0.0a23
+   pypop 1.0.0
+   [Python 3.10.9 | Linux.x86_64-x86_64 | x86_64]
    Copyright (C) 2003-2006 Regents of the University of California.
    Copyright (C) 2007-2023 PyPop team.
    This is free software.  There is NO warranty; not even for
@@ -195,13 +190,7 @@ 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, directly from  `PyPI <https://pypi.org/>`__.
-
-.. warning::
-
-   **These pre-release versions are being made available for initial
-   testing, they are not intended to be used for production
-   applications or analysis**
+directly from  `PyPI <https://pypi.org/>`__.
 
 .. code-block:: shell
 
@@ -258,8 +247,8 @@ general, this is what is wanted, so the above instructions are
 normally sufficient.
 
 However, you can also explicitly set installation to be in the user
-directory, by adding the ``--user`` command-line option to the ``pip
-install`` command, i.e.:
+directory, by adding the ``--user`` command-line option to the ``pip install``
+command, i.e.:
 
 .. code-block:: shell
 
@@ -289,16 +278,18 @@ you need to explicitly provide a URL to the release page.
 
 1. First, visit the release page, and choose the release version you
    wish to install (usually the most recent), and note the release tag
-   (e.g. ``v1.0.0-a23``).
+   (e.g. ``v1.0.0``).
 
    .. admonition:: Release version numbers
 
       Note that version of the release is slightly different to the
       ``git`` tag.  This is because the ``git`` tag follows `Semantic
       Versioning <https://semver.org/>`__, which Python internally
       normalizes and abbreviates.  So the release with the ``git`` tag
-      ``v1.0.0-a23`` is actually version ``1.0.0a23`` of the
-      |pkgname| package, and the version that ``pip`` "sees".
+      ``v1.0.0`` is actually version ``1.0.0`` of the |pkgname|
+      package, and the version that ``pip`` "sees" (the difference is
+      more notable with prereleases which might have a ``git`` tag of
+      ``v1.0.0-rc2`` but the PyPI version will be ``1.0.0rc2``).
 
 2. Next, use ``pip`` to install the package by running a command of
    the form (this will select and install the correct wheel for your
@@ -312,14 +303,14 @@ you need to explicitly provide a URL to the release page.
 
    .. code-block:: shell
    
-      pip install pypop-genomics -f https://github.com/alexlancaster/pypop/releases/expanded_assets/v1.0.0-a23
+      pip install pypop-genomics -f https://github.com/alexlancaster/pypop/releases/expanded_assets/v1.0.0
 
    You can also manually download the specific wheel from the github
    release webpage and install directly, e.g.:
 
    .. 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-1.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
 		
 Post-install ``PATH`` adjustments
 ---------------------------------

website/conf.py

@@ -128,7 +128,7 @@
 #
 html_theme_options = { # these are both piccolo theme-specific
     "source_url": 'https://github.com/alexlancaster/pypop/',
-    "banner_text": 'Release candidates for PyPop are now available via PyPI as package <code>pypop-genomics</code>. See <a href="https://github.com/alexlancaster/pypop#readme">README</a> for more detailed instructions.<br/>'
+    "banner_text": 'PyPop 1.0.0 is released! Install via PyPI: <b><code>pip install pypop-genomics</code></b>.<br/>See <a href="https://github.com/alexlancaster/pypop#readme">README</a> for more detailed installation instructions.<br/>'
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

website/docs/guide-chapter-usage.rst

@@ -53,7 +53,8 @@ In most cases, this will launch a console with the following:
 
 .. code-block:: text
 
-   PyPop: Python for Population Genomics (1.0.0a15)
+   PyPop: Python for Population Genomics (1.0.0)
+   [Python 3.10.9 | Linux.x86_64-x86_64 | x86_64]
    Copyright (C) 2003-2006 Regents of the University of California
    Copyright (C) 2007-2023 PyPop team.
    This is free software.  There is NO warranty; not even for
@@ -97,7 +98,8 @@ absolute) paths to the files. The output should resemble:
 .. code-block:: text
    :emphasize-lines: 14,15
 
-   PyPop: Python for Population Genomics (1.0.0a15)
+   PyPop: Python for Population Genomics (1.0.0)
+   [Python 3.10.9 | Linux.x86_64-x86_64 | x86_64]
    Copyright (C) 2003-2006 Regents of the University of California
    Copyright (C) 2007-2023 PyPop team.
    This is free software.  There is NO warranty; not even for

website/docs/index.rst

@@ -19,13 +19,17 @@ PyPop User Guide
       :start-after: guide-preface-1-start:
       :end-before: guide-preface-1-end:
 
+   .. include:: ../index.rst
+      :start-after: guide-preface-2-start:
+      :end-before: guide-preface-2-end:
+
    .. include:: ../../README.rst
       :start-after: guide-include-pypop-cite-start:
       :end-before: guide-include-pypop-cite-end:
 
    .. include:: ../index.rst
-      :start-after: guide-preface-2-start:
-      :end-before: guide-preface-2-end:
+      :start-after: guide-preface-3-start:
+      :end-before: guide-preface-3-end:
 
 
 **How to use this guide**

website/index.rst

@@ -4,20 +4,29 @@
 PyPop: Python for Population Genomics
 =====================================
 
-.. note::
-
-    Please follow the instructions on the GitHub `README.rst
-    <https://github.com/alexlancaster/pypop#readme>`__ for how to
-    install a 1.0.0 release candidate from PyPI. A formal 1.0.0 release will
-    be made soon.
-
 .. _news:
 
+.. _guide-preface-1-start:
+
+**PyPop (Python for Population Genomics)** is an environment for doing
+large-scale population genetic analyses including:
+
+-  conformity to Hardy-Weinberg expectations
+
+-  tests for balancing or directional selection
+
+-  estimates of haplotype frequencies and measures and tests of
+   significance for linkage disequilibrium (LD).
+
+.. _guide-preface-1-end:
+
 .. admonition:: Release summary and news
-  :class: dropdown, toggle-shown
+  :class: dropdown
 
-  - 2023-11-04: release candidate 2 (1.0.0rc2) is now available on
-    `PyPI <https://pypi.org/project/pypop-genomics/>`__. Fixes some missing TSV output.
+  - 2023-11-07: PyPop 1.0.0 is now available on
+    `PyPI <https://pypi.org/project/pypop-genomics/>`__
+  - 2023-11-04: release candidate 2 (1.0.0rc2) released. Fixes some
+    missing TSV output.
   - 2023-11-01: release candidate 1 (1.0.0rc1) released.
   - 2023-10-27: seventh beta pre-release 1.0.0b7,  Previous ``arm64``
     issues have been resolved. Thanks to Owen Solberg for extensive
@@ -39,37 +48,24 @@ PyPop: Python for Population Genomics
   See the :ref:`PyPop Release History` in the `Python User Guide` for
   earlier history and full release notes.
 
-.. _guide-preface-1-start:
-
-**PyPop (Python for Population Genomics)** is an environment for doing
-large-scale population genetic analyses including:
-
--  conformity to Hardy-Weinberg expectations
-
--  tests for balancing or directional selection
-
--  estimates of haplotype frequencies and measures and tests of
-   significance for linkage disequilibrium (LD).
-
-It is an object-oriented framework implemented in `Python
-<http://www.pypop.org/>`__, a language with powerful features for
-interfacing with other languages, such as C (in which we have already
-implemented many routines and which is particularly suited to
-computationally intensive tasks).
-
-The output of the analyses are stored in XML. These output files can
-then be transformed using standard tools into many other data formats
-suitable for machine input (such as PHYLIP or input for spreadsheet
-programs such as Excel or statistical packages, such as R), plain
-text, or HTML for human-readable format. Storing the output in XML
-allows the final viewable output format to be redesigned at will,
-without requiring the (often time-consuming) re-running of the
-analyses themselves.
+.. _guide-preface-2-start:  
+
+PyPop is an object-oriented framework implemented in `Python
+<http://www.pypop.org/>`__, but also contains C extensions for some
+computationally intensive tasks. Output of analyses are stored in XML
+format for maximum downstream flexibility. PyPop also has an internal
+facility for additionally aggregating the output XML and generating
+output tab-separated (TSV) files, as well as well as generating a
+default plain text file summary for each population.
+
+Although it can be run on any kind of genotype data, it has additional
+support for analyzing population genotype with allelic nomenclature
+from the human leukocyte antigen (HLA) region.
 
 An outline of PyPop can be found in our 2007 *Tissue Antigens* and
 2003 *PSB* :ref:`papers <citing-pypop>`.
 
-.. _guide-preface-1-end:
+.. _guide-preface-2-end:
 
 **Installation and documentation**
 
@@ -86,6 +82,7 @@ PyPop, is contained in the :ref:`PyPop User Guide
    <https://github.com/alexlancaster/pypop/issues>`__. More details on
    how to file bug reports can be found in our :ref:`contributors
    chapter <guide-contributing-bug-report>` of the *User Guide*.
+   Please don't email developers individually.
 
 .. _source-code:
 
@@ -105,7 +102,7 @@ source code is available and maintained on our `GitHub website
    :start-after: guide-include-pypop-cite-start:
    :end-before: guide-include-pypop-cite-end:
 
-.. _guide-preface-2-start:
+.. _guide-preface-3-start:
 
 Also available (but not necessary to cite), is our 2003 *Pacific
 Symposium on Biocomputing* paper:
@@ -134,7 +131,7 @@ IHW) and NIH/NIAID Contract number HHSN266200400076C
 N01-AI-40076. Thanks to Steven J. Mack, Kristie A. Mather, Steve G.E.
 Marsh, Mark Grote and Leslie Louie for helpful comments and testing.
 
-.. _guide-preface-2-end:
+.. _guide-preface-3-end:
 
 .. _popdata-files: