Init from old repo so people can't see my terrible code

.editorconfig

@@ -0,0 +1,16 @@
+# top-most EditorConfig file
+root = true
+
+
+# Match all files...
+[*]
+end_of_line = lf
+
+
+# Python files
+[*.py]
+charset = utf-8
+indent_style = tab
+tab_width = 4
+insert_final_newline = true
+trim_trailing_whitespace = true

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+    env:
+      TESTDB_DIR: tests/data/testdb_210126
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache test database
+      id: cache-test-database
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.TESTDB_DIR }}
+        # Increment the number on the end every time the test data changes
+        key: testdb-data-2
+
+    - name: Download test database
+      if: steps.cache-test-database.outputs.cache-hit != 'true'
+      env:
+        BASE_URL: https://storage.googleapis.com/hesslab-gambit-public/databases/testdb_210126
+      run: |
+        mkdir $TESTDB_DIR/query-seqs
+        wget -O $TESTDB_DIR/testdb_210126-signatures.h5 $BASE_URL/testdb_210126-signatures-210707.h5
+        wget -O - $BASE_URL/testdb_210126_query_seqs.tar.gz | tar -xz -C $TESTDB_DIR/query-seqs
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools Cython numpy pytest
+
+    - name: Build package
+      run: |
+        pip install .
+
+    - name: Test with pytest
+      env:
+        PY_IGNORE_IMPORTMISMATCH: 1
+      run: |
+        pytest --gambit-test-full-db

.gitignore

@@ -0,0 +1,89 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject

MANIFEST.in

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+# Alembic
+include gambit/db/migrate/alembic.ini
+recursive-include gambit/db/migrate *.py

README.md

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+# GAMBIT
+[![Build Status](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml/badge.svg)](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml)
+
+GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens.
+It uses an extremely efficient genomic distance metric along with a curated database of over 50,000 reference genomes (derived from NCBI [RefSeq](https://www.ncbi.nlm.nih.gov/refseq/))
+to identify query genomes within seconds.
+
+Developed by Jared Lumpe in collaboration with the David Hess lab at Santa Clara University.
+
+
+## Installation
+
+### Building from source
+
+Install build dependencies:
+
+    pip install setuptools numpy cython
+
+Clone the repository:
+
+    git clone https://github.com/hesslab-gambit/gambit
+
+Build and install:
+
+    cd gambit
+    pip install .
+
+
+### Database files
+
+TODO
+
+
+## Usage
+
+    gambit [OPTIONS] query [--csv | --json] [-o OUTPUT] GENOMES*
+
+Query genomes must be assembled but may consist of multiple contigs. Currently only FASTA format is supported.
+Support for unassembled raw reads (FASTQ format) is in development.
+
+
+## Contact
+
+For questions regarding usage of the software itself, please contact Jared Lumpe at [[email protected]](mailto:[email protected]).
+All other questions should be directed to David Hess at [[email protected]](mailto:[email protected]).

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'GAMBIT'
+copyright = '2021, Jared Lumpe'
+author = 'Jared Lumpe'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+	'sphinx.ext.autodoc',
+	# 'sphinx.ext.doctest',
+	'sphinx.ext.intersphinx',
+	# 'sphinx.ext.todo',
+	# 'sphinx.ext.coverage',
+	# 'sphinx.ext.mathjax',
+	# 'sphinx.ext.viewcode',
+	'sphinx.ext.napoleon',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/gambit.db.migrate.rst

@@ -0,0 +1,10 @@
+gambit.db.migrate package
+=========================
+
+Module contents
+---------------
+
+.. automodule:: gambit.db.migrate
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/gambit.db.models.rst

@@ -0,0 +1,7 @@
+gambit.db.models module
+=======================
+
+.. automodule:: gambit.db.models
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/gambit.db.rst

@@ -0,0 +1,27 @@
+gambit.db package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   gambit.db.migrate
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   gambit.db.models
+   gambit.db.sqla
+
+Module contents
+---------------
+
+.. automodule:: gambit.db
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/gambit.db.sqla.rst

@@ -0,0 +1,12 @@
+gambit.db.sqla module
+=====================
+
+.. automodule:: gambit.db.sqla
+   :no-members:
+   :show-inheritance:
+
+   .. autoclass:: JsonString
+      :no-inherited-members:
+
+   .. autoclass:: ReadOnlySession
+      :no-inherited-members: