Merge pull request #36 from cgevans/echo

Echo support

.github/workflows/python-package.yml

@@ -19,62 +19,37 @@ on:
       - CHANGELOG.md
       - README.md
       - AUTHORS.md
+concurrency:
+  group: test-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHONUNBUFFERED: "1"
+  FORCE_COLOR: "1"
 jobs:
-  # black:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Set up Python 3.10
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: "3.10"
-  #     - uses: actions/checkout@v3
-  #     - uses: psf/black@stable
-  #       with:
-  #          options: "--check --verbose --diff"
-  #          src: "./src"
-  mypy:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - uses: actions/checkout@v3
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools_scm[toml] wheel setuptools
-          python -m pip install --upgrade attrs types-attrs types-tabulate types-PyYAML types-toml
-          python -m pip install --upgrade mypy
-          python -m pip install --upgrade .
-          mkdir -p .mypy_cache
-      - name: Mypy
-        run: |
-          mypy --cache-dir .mypy_cache --install-types --non-interactive --show-traceback ./src/alhambra_mixes
   tests:
-    #needs: "mypy"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install Hatch
+      run: pip install --upgrade hatch coverage
+    - name: Run tests
       run: |
-        python -m pip install --upgrade pip setuptools_scm[toml] wheel setuptools
-        python -m pip install --upgrade pytest
-        python -m pip install --upgrade .[testing]
-    - name: Test with tox/pytest
-      run: |
-        python -m pytest --cov alhambra_mixes --cov-report=xml
-
+        hatch test --python ${{ matrix.python-version }} --cover --randomize
+        coverage xml
     - name: "Upload coverage to Codecov"
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
         fail_ci_if_error: false

LICENSE.txt

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Constantine Evans and other contributors.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -34,6 +34,11 @@ components at different concentrations spread across several plates.
 
 # Changelog
 
+## v0.6.0
+
+- Optional ECHO liquid handler support, with the 'echo' feature (eg, `pip install --upgrade alhambra_mixes[echo]`).  Uses [kithairon](https://github.com/cgevans/kithairon), which
+  does require Python ≥ 3.10.
+
 ## v0.5.0
 
 An interim version release while larger changes are being made, so that users can make use of several important new features, and the pypi-available version fits well with the latest documentation.

pyproject.toml

@@ -1,10 +1,17 @@
 [build-system]
-requires = ["setuptools>=60", "setuptools_scm[toml]>=8", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
-[tool.setuptools_scm]
-version_scheme = "no-guess-dev"
-write_to = "src/alhambra_mixes/_version.py"
+[tool]
+rye = { dev-dependencies = [
+    "pytest>=8.2.2",
+] }
+
+[tool.hatch]
+version.source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/alhambra_mixes/_version.py"
 
 [tool.pytest.ini_options]
 # addopts = "--cov alhambra --cov-report term-missing --cov-report html"
@@ -14,18 +21,26 @@ norecursedirs = [
     ".tox"]
 testpaths = ["tests"]
 
+[tool.hatch.metadata.hooks.vcs.urls]
+Homepage = "https://github.com/cgevans/mixes"
+Documentation = "https://alhambra-mixes.readthedocs.io"
+Repository = "https://github.com/cgevans/mixes.git"
+Issues = "https://github.com/cgevans/issues"
+source_archive = "https://github.com/org/repo/archive/{commit_hash}.zip"
+
 [project]
 name = "alhambra_mixes"
-dynamic = ["version"]
+dynamic = ["version", "urls"]
 description = "Many-component mix library for molecular programming"
 authors = [{name = "Constantine Evans", email="[email protected]"}]
-license = { file = "LICENCE.txt" }
+license = { file = "LICENSE.txt" }
 classifiers = [
     "Development Status :: 4 - Beta",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
@@ -36,11 +51,13 @@ dependencies = [
     "pandas",
     "openpyxl",
     "pint >= 0.20",
+    "polars ~= 0.20.7",
     "tabulate",
     "toml",
-    "typing_extensions >= 4.2"
+    "typing_extensions >= 4.2",
 ]
 readme = "README.md"
+requires-python = ">= 3.8"
 
 [project.optional-dependencies]
 docs = [
@@ -55,15 +72,19 @@ testing = [
     "pytest",
     "pytest-cov"
 ]
+echo = [
+    "kithairon >= 0.2.0",
+]
+all = [
+    "alhambra_mixes[echo]"
+]
 
 
 [tool.setuptools.packages.find]
 where = ["src"]
 
-
-
 [tool.black]
-target_version = ["py39"]
+target-version = ["py312"]
 
 [tool.mypy]
 python_version = "3.9"
@@ -72,3 +93,25 @@ warn_unused_configs = true
 ignore_missing_imports = true
 #disallow_untyped_defs = true
 #disallow_incomplete_defs = true
+
+[tool.hatch.envs.hatch-test]
+dependencies = [
+"pytest",
+"pytest-cov",
+]
+
+[tool.hatch.envs.hatch-test.overrides]
+name.echo.features = ["echo"]
+
+[[tool.hatch.envs.hatch-test.matrix]]
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+[[tool.hatch.envs.hatch-test.matrix]]
+python = ["3.10", "3.11", "3.12"]
+feature = ["echo"]
+
+[tool.ruff]
+ignore = ["TID252", "N816", "F405", "F403", "ARG002"
+    # For now
+    , "EM101", "EM102", "RET505", "RET504", "TRY003", "PLR2004"
+]

src/alhambra_mixes/CHANGELOG.md

@@ -0,0 +1,5 @@
+# ???
+
+- Make null-plate for component be None, not "".  This is ultimately safer in forcing handling of unspecified plates.
+- Adding location information.
+- Echo support.

src/alhambra_mixes/__init__.py

@@ -1,13 +1,21 @@
-from .actions import *
-from .components import *
+from .actions import (
+    AbstractAction,
+    EqualConcentration,
+    FixedConcentration,
+    FixedVolume,
+    MultiFixedConcentration,
+    MultiFixedVolume,
+    ToConcentration,
+)
+from .components import AbstractComponent, Component, Strand
 from .experiments import Experiment
-from .mixes import *
-from .printing import *
-from .quantitate import *
-from .references import *
-from .units import *
+from .locations import WellPos
+from .mixes import Mix, MixLine, master_mix, split_mix
+from .quantitate import hydrate_and_measure_conc_and_dilute, measure_conc_and_dilute
+from .references import Reference, load_reference
+from .units import DNAN, Q_, VolumeError, nM, uL, uM, ureg
 
-__all__ = (
+__all__ = [
     "uL",
     "uM",
     "nM",
@@ -29,11 +37,32 @@
     "MixLine",
     "Reference",
     "load_reference",
-    #    "_format_title",
     "DNAN",
     "VolumeError",
-    #    "D",
     "measure_conc_and_dilute",
     "hydrate_and_measure_conc_and_dilute",
     "split_mix",
-)
+    "master_mix",
+]
+
+try:
+    from .echo import (
+        AbstractEchoAction,
+        EchoEqualTargetConcentration,
+        EchoFillToVolume,
+        EchoFixedVolume,
+        EchoTargetConcentration,
+    )
+
+    __all__ += [
+        "EchoEqualTargetConcentration",
+        "EchoFillToVolume",
+        "EchoFixedVolume",
+        "EchoTargetConcentration",
+        "AbstractEchoAction"
+    ]
+except ImportError as err:
+    if err.name == "kithairon":
+        pass
+    else:
+        raise err # noqa

src/alhambra_mixes/abbreviated.py

@@ -1,11 +1,10 @@
-from re import L
 
 from .actions import *
 from .components import *
+from .experiments import Experiment
 from .mixes import *
 from .references import *
 from .units import *
-from .experiments import Experiment
 
 __all__ = (
     "Q_",
@@ -36,7 +35,6 @@
 S = Strand
 C = Component
 Ref = Reference
-Mix = Mix
 Exp = Experiment
 
 µM = ureg.Unit("µM")