pyham 1.2.0__tar.gz → 2.0.0__tar.gz

pyham-2.0.0/.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

pyham-2.0.0/.github/workflows/python-package.yml

@@ -0,0 +1,69 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build Python package and run tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ matrix.experimental || false }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        experimental: [false]
+        include:
+          - python-version: "3.15-dev"
+            experimental: true
+
+    steps:
+    - uses: actions/checkout@v7
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v7
+      with:
+        python-version: ${{ matrix.python-version }}
+        allow-prereleases: true
+    - name: Install libxml2/libxslt headers (no lxml wheel yet for this Python build)
+      if: matrix.experimental
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libxml2-dev libxslt-dev
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest -v
+
+  docs:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v7
+      with:
+        fetch-depth: 0  # setuptools_scm needs the tags to determine the version
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install ".[docs]"
+    - name: Build documentation (warnings are errors, as on Read the Docs)
+      run: |
+        sphinx-build -W --keep-going -b html docs docs/_build/html

pyham-2.0.0/.github/workflows/python-publish.yml

@@ -0,0 +1,33 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - uses: actions/checkout@v7
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33
+

pyham-2.0.0/.gitignore

@@ -0,0 +1,10 @@
+build
+dist
+*/__pycache__
+*.egg-info
+*.pyc
+.ropeproject
+.idea
+.ipynb_checkpoints
+pyham/_version.py
+docs/_build

pyham-2.0.0/.readthedocs.yaml

@@ -0,0 +1,22 @@
+# Read the Docs configuration, see https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_checkout:
+      # setuptools_scm derives the version from git tags, which a shallow clone lacks
+      - git fetch --unshallow --tags || true
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

{pyham-1.2.0/pyham.egg-info → pyham-2.0.0}/PKG-INFO

@@ -1,45 +1,41 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pyham
-Version: 1.2.0
+Version: 2.0.0
 Summary: A tool to analyse Hierarchical Orthologous Groups (HOGs)
-Home-page: http://lab.dessimoz.org/ham
-Author: Dessimoz Lab - Laboratory of Computational Evolutionary Biology and Genomics
-Author-email: adrian.altenhoff@inf.ethz.ch
-License: MIT
-Keywords: orthology, HOGs, orthoxml
+Author-email: Dessimoz Lab - Laboratory of Computational Evolutionary Biology and Genomics <adrian.altenhoff@inf.ethz.ch>
+License-Expression: MIT
+Project-URL: Homepage, http://lab.dessimoz.org/ham
+Keywords: orthology,HOGs,orthoxml
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
-Requires-Dist: ete3>=3.1
-Requires-Dist: six
+Requires-Dist: ete4>=4.3
 Requires-Dist: lxml
-Requires-Dist: future
 Requires-Dist: requests
 Requires-Dist: tqdm
 Requires-Dist: scipy
 Provides-Extra: test
-Requires-Dist: nose; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
 Provides-Extra: dev
-Requires-Dist: nose; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
 Requires-Dist: sphinx; extra == "dev"
 Requires-Dist: wheel; extra == "dev"
 Requires-Dist: twine; extra == "dev"
-Requires-Dist: fabric; extra == "dev"
-Requires-Dist: fabric3; extra == "dev"
+Dynamic: license-file
 
 pyHam: A Tool to Analyze Hierarchical Orthologous Groups (HOGs)
 ===============================================================
@@ -65,23 +61,50 @@ If you use pyHam in your work, please consider citing:
 
 Installation
 ------------
-Ham is written in python3 (also compatible with python2), with little external dependencies, i.e.
-currently ete3, lml, six. The setup script should resolve these
-dependencies automatically.
-Consider using pip to install the package directly from a checked out git repo
+pyHam requires Python 3.9 or newer. Its dependencies (ete4, lxml, requests, tqdm and scipy)
+are installed automatically by pip:
 
 .. code-block:: sh
 
    python -m pip install --upgrade pip
    pip install pyham
 
+To work on pyHam itself, install it in editable mode from a checkout of the git repository:
+
+.. code-block:: sh
+
+   python -m pip install -e ".[dev]"
+   pytest
+
+Quick start
+-----------
+
+.. code-block:: python
+
+   import pyham
+
+   ham = pyham.Ham("simpleEx.phyloxml", "simpleEx.orthoxml",
+                   tree_format="phyloxml", use_internal_name=True)
+
+   # look up a gene family (HOG) and export it as a gene tree
+   hog = ham.get_hog_by_id("HOG:0355161")
+   print(hog.to_ete_tree().write())
+
+   # compare a species with one of its ancestors
+   human = ham.get_extant_genome_by_name("Homo sapiens")
+   primates = ham.get_ancestral_genome_by_name("Primates")
+   vmap = ham.compare_genomes_vertically(human, primates)
+   print(len(vmap.get_retained()), len(vmap.get_duplicated()),
+         len(vmap.get_lost()), len(vmap.get_gained()))
+
 Example
 -------
-We prepare a ready-to-use example (see example folder) with few python scripts to use main pyHam features.
-You just have to run the following command in bash:
+The ``example`` folder contains a few ready-to-use scripts that show the main pyHam features.
+Run them from inside that folder:
 
 .. code-block:: sh
 
+   cd example
    python run_hog_queries.py
    python run_treeProfile.py
    python run_iHam.py
@@ -104,13 +127,16 @@ Support for pyHam by various HOG inference resources.
 +-----------------+------------------------------+---------------------------------------+-----------+
 ||OMA standalone|_| PhyloXML and Newick          | All HOGs                              |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
+| |FastOMA|_      | Newick                       | All HOGs                              |    YES    |
++-----------------+------------------------------+---------------------------------------+-----------+
 | |Ensembl|_      | |Newicke|_                   |    one HOG at a time                  |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
-| |HieranoidDB|_  | |Newickh|_                   |    one HOG at a time                  |    YES    |
+| |HieranoidDB|_  | Newick                       |    one HOG at a time                  |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
 
 .. |OMA browser| replace:: ``OMA browser``
 .. |OMA standalone| replace:: ``OMA standalone``
+.. |FastOMA| replace:: ``FastOMA``
 .. |Ensembl| replace:: ``Ensembl``
 .. |HieranoidDB| replace:: ``HieranoidDB``
 
@@ -119,27 +145,56 @@ Support for pyHam by various HOG inference resources.
 .. |PhyloXMLs| replace:: ``PhyloXML``
 .. |Newicks| replace:: ``Newick``
 .. |Newicke| replace:: ``Newick``
-.. |Newickh| replace:: ``Newick``
 
 .. |All HOGso| replace:: ``All HOGs``
 .. |one HOG at a timeo| replace:: ``one HOG at a time``
 
 .. _OMA browser: https://omabrowser.org
 .. _OMA standalone: https://omabrowser.org/standalone/
+.. _FastOMA: https://github.com/DessimozLab/FastOMA
 .. _Ensembl: https://www.ensembl.org/index.html
 .. _HieranoidDB: http://hieranoidb.sbc.su.se/
 
 .. _PhyloXMLo: https://omabrowser.org/All/speciestree.phyloxml
 .. _Newicko: https://omabrowser.org/All/speciestree.nwk
 .. _Newicke: https://www.ensembl.org/info/about/speciestree.html
-.. _Newickh: http://hieranoid.sbc.su.se/download/H2/66c.tree
 
 .. _All HOGso:  https://omabrowser.org/All/oma-hogs.orthoXML.gz
 .. _one HOG at a timeo:  https://omabrowser.org/oma/hogs/
 
 
+Common input problems
+---------------------
+Most errors when loading data come from a species tree that doesn't match the OrthoXML file.
+To check your inputs before analysing them, run:
+
+.. code-block:: sh
+
+   pyham-validate species_tree.nwk hogs.orthoxml
+
+or, from Python, ``print(pyham.validate_input(tree_file, hog_file, ...))``, which takes the same
+arguments as ``pyham.Ham``. It reports every problem it finds at once, each with the affected species,
+levels or families and, where it can tell, how to fix it. The most common problems are:
+
+- **Use the species tree the HOGs were inferred with.** pyHam maps each HOG onto the species
+  tree, so the tree must contain every species in the OrthoXML file under the same name, and
+  its topology must agree with how the HOGs are nested. With OMA standalone and FastOMA, use the
+  species tree written alongside the HOGs.
+- **use_internal_name=True needs unique internal node names.** Some newick trees label internal
+  nodes with numbers (e.g. support values) instead of taxon names. pyHam then reports that the
+  internal names are not unique. Pass ``use_internal_name=False`` and pyHam will build names
+  from the child species instead.
+- **PhyloXML trees need a name field on every node.** Choose the field with
+  ``phyloxml_leaf_name_tag`` and ``phyloxml_internal_name_tag``. If the tree has no
+  ``<taxonomy>`` elements, use ``clade_name``, or pass ``use_internal_name=False``.
+- **Taxonomic conflicts.** If a HOG's taxonomic range (``TaxRange`` or taxid) disagrees with
+  the species tree, pyHam raises ``TaxonomicConflictError`` listing every conflicting family it
+  found. Pass ``fail_fast=True`` to stop at the first one.
+- **Singletons.** Genes that belong to no HOG can be looked up with ``get_gene_by_id``, but
+  HOG-based tools such as tree profiles and iHam don't apply to them.
+
 Documentation
 -------------
-You can the full documentation of pyHam at http://zoo.cs.ucl.ac.uk/doc/pyham/index.html
+The full documentation of pyHam, including the API reference, is available at https://pyham-dessimozlab.readthedocs.io.
 
 

{pyham-1.2.0 → pyham-2.0.0}/README.rst

@@ -22,23 +22,50 @@ If you use pyHam in your work, please consider citing:
 
 Installation
 ------------
-Ham is written in python3 (also compatible with python2), with little external dependencies, i.e.
-currently ete3, lml, six. The setup script should resolve these
-dependencies automatically.
-Consider using pip to install the package directly from a checked out git repo
+pyHam requires Python 3.9 or newer. Its dependencies (ete4, lxml, requests, tqdm and scipy)
+are installed automatically by pip:
 
 .. code-block:: sh
 
    python -m pip install --upgrade pip
    pip install pyham
 
+To work on pyHam itself, install it in editable mode from a checkout of the git repository:
+
+.. code-block:: sh
+
+   python -m pip install -e ".[dev]"
+   pytest
+
+Quick start
+-----------
+
+.. code-block:: python
+
+   import pyham
+
+   ham = pyham.Ham("simpleEx.phyloxml", "simpleEx.orthoxml",
+                   tree_format="phyloxml", use_internal_name=True)
+
+   # look up a gene family (HOG) and export it as a gene tree
+   hog = ham.get_hog_by_id("HOG:0355161")
+   print(hog.to_ete_tree().write())
+
+   # compare a species with one of its ancestors
+   human = ham.get_extant_genome_by_name("Homo sapiens")
+   primates = ham.get_ancestral_genome_by_name("Primates")
+   vmap = ham.compare_genomes_vertically(human, primates)
+   print(len(vmap.get_retained()), len(vmap.get_duplicated()),
+         len(vmap.get_lost()), len(vmap.get_gained()))
+
 Example
 -------
-We prepare a ready-to-use example (see example folder) with few python scripts to use main pyHam features.
-You just have to run the following command in bash:
+The ``example`` folder contains a few ready-to-use scripts that show the main pyHam features.
+Run them from inside that folder:
 
 .. code-block:: sh
 
+   cd example
    python run_hog_queries.py
    python run_treeProfile.py
    python run_iHam.py
@@ -61,13 +88,16 @@ Support for pyHam by various HOG inference resources.
 +-----------------+------------------------------+---------------------------------------+-----------+
 ||OMA standalone|_| PhyloXML and Newick          | All HOGs                              |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
+| |FastOMA|_      | Newick                       | All HOGs                              |    YES    |
++-----------------+------------------------------+---------------------------------------+-----------+
 | |Ensembl|_      | |Newicke|_                   |    one HOG at a time                  |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
-| |HieranoidDB|_  | |Newickh|_                   |    one HOG at a time                  |    YES    |
+| |HieranoidDB|_  | Newick                       |    one HOG at a time                  |    YES    |
 +-----------------+------------------------------+---------------------------------------+-----------+
 
 .. |OMA browser| replace:: ``OMA browser``
 .. |OMA standalone| replace:: ``OMA standalone``
+.. |FastOMA| replace:: ``FastOMA``
 .. |Ensembl| replace:: ``Ensembl``
 .. |HieranoidDB| replace:: ``HieranoidDB``
 
@@ -76,27 +106,56 @@ Support for pyHam by various HOG inference resources.
 .. |PhyloXMLs| replace:: ``PhyloXML``
 .. |Newicks| replace:: ``Newick``
 .. |Newicke| replace:: ``Newick``
-.. |Newickh| replace:: ``Newick``
 
 .. |All HOGso| replace:: ``All HOGs``
 .. |one HOG at a timeo| replace:: ``one HOG at a time``
 
 .. _OMA browser: https://omabrowser.org
 .. _OMA standalone: https://omabrowser.org/standalone/
+.. _FastOMA: https://github.com/DessimozLab/FastOMA
 .. _Ensembl: https://www.ensembl.org/index.html
 .. _HieranoidDB: http://hieranoidb.sbc.su.se/
 
 .. _PhyloXMLo: https://omabrowser.org/All/speciestree.phyloxml
 .. _Newicko: https://omabrowser.org/All/speciestree.nwk
 .. _Newicke: https://www.ensembl.org/info/about/speciestree.html
-.. _Newickh: http://hieranoid.sbc.su.se/download/H2/66c.tree
 
 .. _All HOGso:  https://omabrowser.org/All/oma-hogs.orthoXML.gz
 .. _one HOG at a timeo:  https://omabrowser.org/oma/hogs/
 
 
+Common input problems
+---------------------
+Most errors when loading data come from a species tree that doesn't match the OrthoXML file.
+To check your inputs before analysing them, run:
+
+.. code-block:: sh
+
+   pyham-validate species_tree.nwk hogs.orthoxml
+
+or, from Python, ``print(pyham.validate_input(tree_file, hog_file, ...))``, which takes the same
+arguments as ``pyham.Ham``. It reports every problem it finds at once, each with the affected species,
+levels or families and, where it can tell, how to fix it. The most common problems are:
+
+- **Use the species tree the HOGs were inferred with.** pyHam maps each HOG onto the species
+  tree, so the tree must contain every species in the OrthoXML file under the same name, and
+  its topology must agree with how the HOGs are nested. With OMA standalone and FastOMA, use the
+  species tree written alongside the HOGs.
+- **use_internal_name=True needs unique internal node names.** Some newick trees label internal
+  nodes with numbers (e.g. support values) instead of taxon names. pyHam then reports that the
+  internal names are not unique. Pass ``use_internal_name=False`` and pyHam will build names
+  from the child species instead.
+- **PhyloXML trees need a name field on every node.** Choose the field with
+  ``phyloxml_leaf_name_tag`` and ``phyloxml_internal_name_tag``. If the tree has no
+  ``<taxonomy>`` elements, use ``clade_name``, or pass ``use_internal_name=False``.
+- **Taxonomic conflicts.** If a HOG's taxonomic range (``TaxRange`` or taxid) disagrees with
+  the species tree, pyHam raises ``TaxonomicConflictError`` listing every conflicting family it
+  found. Pass ``fail_fast=True`` to stop at the first one.
+- **Singletons.** Genes that belong to no HOG can be looked up with ``get_gene_by_id``, but
+  HOG-based tools such as tree profiles and iHam don't apply to them.
+
 Documentation
 -------------
-You can the full documentation of pyHam at http://zoo.cs.ucl.ac.uk/doc/pyham/index.html
+The full documentation of pyHam, including the API reference, is available at https://pyham-dessimozlab.readthedocs.io.
 
 

pyham-2.0.0/ReleaseNotes.txt

@@ -0,0 +1,201 @@
+
+########################################################################################
+
+VERSION 1.2.0
+
+FIX:
+    - Remove unnecessary files from git repo
+    - replace outdated nosetests -> pytest as test running
+
+IMPROVEMENTS:
+    - Improve handling of HOG IDs in pyham. HOG objects use "hog_id" or "og" attribute 
+      from orthoxml to show objects, and also include the taxonomic range.
+    - LOFT attribute will be loaded for gene elements if assigned in orthoxml.
+
+
+
+########################################################################################
+
+VERSION 1.1.12
+
+FIX:
+    - Fix issue of OrthoXML_manager.get_orthoxml_str not creating orthologous group if only content paralogous groups inside.
+
+IMPROVEMENTS:
+    - Update iHam libraries to latest
+
+########################################################################################
+
+VERSION 1.1.7
+
+FIX:
+    - Fix issue with retrieving the correct species tree for a ham analysis if run 
+      from remote datasource (oma server). (Fixes github issue #2)
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################
+
+VERSION 1.1.6
+
+FIX:
+    - Fix duplicated items in duplicationNode children for complex paralogous cases.
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################
+
+VERSION 1.1.5
+
+FIX:
+    - Fix iHam (keep use the d3.v3 instead of d3.v5).
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################
+
+VERSION 1.1.4
+
+FIX:
+    - Remote js library not loaded when opening iham or tree profile html output file.
+
+IMPROVEMENTS:
+    - Add possibility to load one hog for remote database by single gene query (only oma for now)
+    - TreeProfile: Make visualisation clearer.
+
+########################################################################################
+
+VERSION 1.1.3
+
+FIX:
+    - Fix Bytes Error for phyloxml in python 3.
+
+IMPROVEMENTS:
+    - Add few option to improve selection of xml tag in phyloxml for extant and ancestral
+     species names.
+
+########################################################################################
+
+VERSION 1.1.2
+
+FIX:
+    - Bug ancestral name were not set correctly using phyloxml taxonomy scientific name tag
+
+IMPROVEMENTS:
+    - None.
+
+########################################################################################
+
+VERSION 1.1.1
+
+FIX:
+    - None
+
+IMPROVEMENTS:
+    - Tree Profile: Add help modal.
+    - iHam: Update settings.
+
+########################################################################################
+
+VERSION 1.1.0
+
+FIX:
+    - None
+
+IMPROVEMENTS:
+    - Tree Profile: add option to switch between number of genes resulting of each types of phylogenetic events or number of
+    phylogenetic events (NEW)
+    - Tree Profile: add few customisation options (Hide/Show elements, switch between fixed size of stacks or based on genome sizes)
+    - Add UnitTest for iHam
+    - Add number of duplication events in VerticalMapper.
+    - Add phyloXML as input format for phylogeny.
+
+########################################################################################
+
+VERSION 1.0.9
+
+FIX:
+    - None
+
+IMPROVEMENTS:
+    - Tree profile: add scale bar, remove level annotations for taxonomic range without ancestral genes.
+    - For clarity purposes, genes that don't duplicate or get lost between two taxon are now denoted as 'retained' instead of 'identical'.
+
+########################################################################################
+
+VERSION 1.0.8
+
+FIX:
+    - fix secure duplication handling fix.
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################
+
+VERSION 1.0.6
+
+FIX:
+    - secure duplication handling.
+
+IMPROVEMENTS:
+    - None
+
+
+########################################################################################
+
+VERSION 1.0.5
+
+FIX:
+    - Fix single HOG orthoXMLformating for iHam.
+
+IMPROVEMENTS:
+    - None
+
+
+########################################################################################
+
+VERSION 1.0.4
+
+FIX:
+    - iHam compatible for p2 and p3.
+
+IMPROVEMENTS:
+    - None
+
+
+########################################################################################
+
+VERSION 1.0.2
+
+FIX:
+    - UnitTesting module compatible for p2 and p3.
+
+IMPROVEMENTS:
+    - None
+
+
+########################################################################################
+
+VERSION 1.0.1
+
+FIX:
+    - OrthoXML parser raise useless 'ValueError: Minimum 2 genomes are required, only 1 provided.' for highly duplicated HOGs.
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################
+
+VERSION 1.0.0 - Official release
+
+FIX:
+    - None
+
+IMPROVEMENTS:
+    - None
+
+########################################################################################

{pyham-1.2.0 → pyham-2.0.0}/docs/api.rst

@@ -16,6 +16,7 @@ Here is the documentation for the Ham objects.
    utils
    treeprofile
    iHam
+   validation