Merge latest into fork

.github/workflows/ci.yml

@@ -11,26 +11,33 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10', 3.11]
+        python-version: [3.9, '3.10', 3.11, 3.12, 3.13]
+        sqla-version: ["~=2.0"]
+        include:
+          # Also test with SQLALchemy >=1.4, <2
+          - python-version: 3.12
+            sqla-version: "~=1.4"
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: |
+          pyproject.toml
+          setup.cfg
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install setuptools pytest
+        python -m pip install setuptools pytest sqlalchemy${{ matrix.sqla-version }}
 
     - name: Build package
       run: |
         pip install .
 
     - name: Test with pytest
-      env:
-        PY_IGNORE_IMPORTMISMATCH: 1
       run: |
         pytest

CHANGELOG.md

@@ -1,11 +1,25 @@
 # Changelog
 
 
+## 1.1.0
+
+* Command line interface:
+  * Better error reporting when database file(s) not found
+  * Add more details to output of `gambit signatures info` command.
+* Major overhaul of internal Python API and tests (see full release notes on GitHub)
+  * Many fixes to API documentation
+* Increase minimum Python version to 3.9
+* Make compatible with SQLAlchemy 2.0
+
+
 ## 1.0.1
 
+* Significant documentation updates.
+* Better error reporting:
+  * When database files cannot be found (in CLI and API).
+  * On attempting to open an invalid signatures file.
 * Misc
-  * Better error reporting when database files cannot be found (in CLI and API).
-  * Minor documentation updates.
+  * Run tests on Python 3.11 and 3.12.
 
 
 ## 1.0.0

MANIFEST.in

@@ -1,3 +1,2 @@
-# Alembic
-include gambit/db/migrate/alembic.ini
-recursive-include gambit/db/migrate *.py
+graft src
+graft docs

README.md

@@ -13,6 +13,17 @@ See below for basic installation and usage instructions, or check out the
 a basic tutorial.
 
 
+## About
+
+Copyright © 2016-2024 Jared Lumpe
+
+GAMBIT has been a personal project of mine for many years. Although there have been numerous
+contributors to the publication, it is not a product of any lab or institution.
+
+GAMBIT is provided as free software under the terms of the [AGPLv3 license](LICENSE).
+It is not covered by any type of software patent.
+
+
 ### Publication
 
 Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, et al. (2023) GAMBIT (Genomic Approximation

docs/source/api/database.rst

@@ -32,9 +32,3 @@ gambit.db.sqla
    .. autoclass:: ReadOnlySession
       :exclude-members: __init__, __new__
       :no-members:
-
-
-gambit.db.migrate
------------------
-
-.. automodule:: gambit.db.migrate

docs/source/api/kmers.rst

@@ -27,6 +27,7 @@ gambit.sigs.base
 ----------------------
 
 .. automodule:: gambit.sigs.base
+   :exclude-members: AbstractSignatureArray
 
    .. autoclass:: AbstractSignatureArray
       :special-members: +__eq__
@@ -38,16 +39,11 @@ gambit.sigs.calc
 .. automodule:: gambit.sigs.calc
 
 
-gambit.sigs.convert
--------------------------
-
-.. automodule:: gambit.sigs.convert
-
-
 gambit.sigs.hdf5
 ----------------------
 
 .. automodule:: gambit.sigs.hdf5
+   :exclude-members: HDF5Signatures
 
    .. autoclass:: HDF5Signatures
       :special-members: +__bool__

docs/source/api/metric.rst

@@ -5,7 +5,3 @@ gambit.metric
 -------------
 
 .. automodule:: gambit.metric
-
-   .. autofunction:: gambit.metric.jaccard
-
-   .. autofunction:: gambit.metric.jaccarddist

docs/source/api/misc.rst

@@ -14,12 +14,6 @@ gambit.util.misc
 .. automodule:: gambit.util.misc
 
 
-gambit.util.typing
-------------------
-
-.. automodule:: gambit.util.typing
-
-
 gambit.util.io
 --------------
 
@@ -36,15 +30,13 @@ gambit.util.indexing
 --------------------
 
 .. automodule:: gambit.util.indexing
+    :exclude-members: AdvancedIndexingMixin
+
+    .. autoclass:: AdvancedIndexingMixin
+        :private-members: _check_index, _getitem_int, _getitem_slice, _getitem_int_array, _getitem_bool_array
 
 
 gambit.util.progress
 --------------------
 
 .. automodule:: gambit.util.progress
-
-
-gambit.util.dev
-----------------
-
-.. automodule:: gambit.util.dev

docs/source/api/results.rst

@@ -6,27 +6,3 @@ gambit.results
 -----------------
 
 .. automodule:: gambit.results
-
-
-gambit.results.base
-----------------------
-
-.. automodule:: gambit.results.base
-
-
-gambit.results.json
-----------------------
-
-.. automodule:: gambit.results.json
-
-
-gambit.results.csv
----------------------
-
-.. automodule:: gambit.results.csv
-
-
-gambit.results.archive
--------------------------
-
-.. automodule:: gambit.results.archive

docs/source/conf.py

@@ -18,11 +18,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'GAMBIT'
-copyright = '2021 - 2023, Jared Lumpe'
+copyright = '2021 - 2024, Jared Lumpe'
 author = 'Jared Lumpe'
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.1'
+release = '1.1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -50,6 +50,17 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
+# When debugging broken cross references using nitpick mode (-n option), ignore these errors.
+# This mostly relates to external libraries that have not been linked to using intersphinx.
+nitpick_ignore_regex = [
+	('py:.*', r'click\..*'),
+	('py:.*', r'sqlalchemy\..*'),
+	('py:.*', r'h5py\..*'),
+	('py:.*', r'scipy\..*'),
+	# TypeVar
+	('py:.*', r'(.*\.)?T\d?'),
+]
+
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -77,4 +88,15 @@
 autodoc_member_order = 'groupwise'
 autodoc_typehints = 'description'
 
+autodoc_type_aliases = {
+    'FilePath': 'FilePath',
+    'DNASeq': 'DNASeq',
+}
+
+intersphinx_mapping = {
+	'python': ('https://docs.python.org/3', None),
+	'numpy': ('https://numpy.org/doc/stable/', None),
+	'Bio': ('https://biopython.org/docs/latest/', None),
+}
+
 todo_include_todos = True