Rename package to macta-tools

The new plan is to separate MACTA's functionality into a different
package. This is mainly for containerization - we can create a container
specifically for the functionality, then call it from the main scripts.

.gitignore

@@ -5,6 +5,7 @@
 __pycache__
 .pytest_cache
 *.egg-info
+Pipfile.lock
 
 .coverage
 .tox

Pipfile

@@ -5,12 +5,12 @@ name = "pypi"
 
 [packages]
 anndata = "==0.8.0"
-celltypist = "==1.3.0"
+# celltypist = "==1.3.0"
 pandas = "==2.0.0"
 pydantic = ">=2.0"
 scanpy = "*"
-scvi-tools = "*"
-scarches = "*"
+# scvi-tools = "*"
+# scarches = "*"
 
 [dev-packages]
 flake8 = "*"

README.md

@@ -9,9 +9,8 @@ The goal of this code is to assemble multiple python-based cell type annotation
 
 ```bash
 git clone https://github.com/AleksBekker/MACTA_py
-cd MACTA_py
-# conda create -n macta_py python=3.7
-pip install -e .
+pipenv install -d
+pipenv run pip install ".[EXTRAS_YOU_WILL_BE_USING]"
 ```
 
 ## Citations
@@ -59,7 +58,5 @@ pip install -e .
 Please refer to the repo's dependency tree (github.com/AleksBekker/MACTA_py/network/dependencies) 
 for information on all other packages used, including: 
 
-- Autopep8
 - Pandas
-
-
+- Pydantic

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "macta"
+name = "macta_tools"
 version = "0.0.4"
 authors = [{ name = "Aleksandr Bekker", email = "alekso.bekker@gmail.com" }]
 description = "Annotation tools for the MACTA suite"
@@ -34,10 +34,10 @@ celltypist = ["celltypist>=1.3.0"]
 scanvi = ["scvi-tools", "scarches"]
 
 # Per-version extras
-py38 = ["macta[celltypist]"]
-py39 = ["macta[celltypist]"]
-py310 = ["macta[celltypist]"]
-torch38 = ["macta[scanvi]"]
+py38 = ["macta_tools[celltypist]"]
+py39 = ["macta_tools[celltypist]"]
+py310 = ["macta_tools[celltypist]"]
+torch38 = ["macta_tools[scanvi]"]
 
 # Testing extras
 testing = [
@@ -52,14 +52,14 @@ testing = [
 
 [tool.setuptools.packages.find]
 where = ["src"]
-include = ["macta*"]
+include = ["macta_tools*"]
 namespaces = false
 
 [tool.setuptools.package-data]
 "pkgname" = ["py.typed"]
 
 [tool.pytest.ini_options]
-addopts = "--cov=macta"
+addopts = "--cov=macta_tools"
 testpaths = ["tests"]
 
 [tool.mypy]

src/macta_tools/__init__.py

@@ -0,0 +1,5 @@
+from macta_tools import tools, utils
+from macta_tools._annotate import annotate
+from macta_tools._cli import run_from_cli
+
+__all__ = ['annotate', 'tools', 'utils', 'run_from_cli']

src/macta/_annotate.py → src/macta_tools/_annotate.py

@@ -6,7 +6,7 @@
 import pandas as pd
 from anndata import AnnData
 
-from macta.tools import AVAILABLE, CTAToolInterface
+from macta_tools.tools import AVAILABLE, CTAToolInterface
 
 
 def annotate(expr_data: AnnData, ref_data: Union[AnnData, pd.DataFrame], annot_type: str, result_type: str = 'labels',

src/macta/tools/__init__.py → src/macta_tools/tools/__init__.py

@@ -1,18 +1,18 @@
 from contextlib import suppress
 from typing import Dict
 
-from macta.tools._cta_tool_interface import CTAToolInterface
+from macta_tools.tools._cta_tool_interface import CTAToolInterface
 
 AVAILABLE: Dict[str, CTAToolInterface] = {}
 __all__ = ['AVAILABLE', 'CTAToolInterface']
 
 
 with suppress(ImportError):
-    from macta.tools._celltypist_interface import CelltypistInterface
+    from macta_tools.tools._celltypist_interface import CelltypistInterface
     __all__.append('CelltypistInterface')
     AVAILABLE['celltypist'] = CelltypistInterface()
 
 with suppress(ImportError):
-    from macta.tools._scanvi import ScanviInterface
+    from macta_tools.tools._scanvi import ScanviInterface
     __all__.append('ScanviInterface')
     AVAILABLE['scanvi'] = ScanviInterface()

src/macta/tools/_celltypist_interface.py → src/macta_tools/tools/_celltypist_interface.py

@@ -10,8 +10,8 @@
 from celltypist import models
 from celltypist.classifier import AnnotationResult
 
-from macta.tools._cta_tool_interface import CTAToolInterface
-from macta.utils.requirements import EqualityRequirement, RequirementList
+from macta_tools.tools._cta_tool_interface import CTAToolInterface
+from macta_tools.utils.requirements import EqualityRequirement, RequirementList
 
 # Disable `celltypist`'s trivial output logs
 logging.getLogger(celltypist.__name__).setLevel(logging.ERROR)

src/macta/tools/_cta_tool_interface.py → src/macta_tools/tools/_cta_tool_interface.py

@@ -5,7 +5,7 @@
 
 import pandas as pd
 
-from macta.utils.requirements import RequirementList
+from macta_tools.utils.requirements import RequirementList
 
 
 class CTAToolInterface(ABC):

src/macta/tools/_scanvi.py → src/macta_tools/tools/_scanvi.py

@@ -5,9 +5,9 @@
 import pandas as pd
 from scanpy import AnnData
 
-from macta.tools._cta_tool_interface import CTAToolInterface
-from macta.utils.contexts import suppress_logging
-from macta.utils.requirements import EqualityRequirement, NotNoneRequirement, RequirementList
+from macta_tools.tools._cta_tool_interface import CTAToolInterface
+from macta_tools.utils.contexts import suppress_logging
+from macta_tools.utils.requirements import EqualityRequirement, NotNoneRequirement, RequirementList
 
 # Suppress the output that comes with importing scArches
 with suppress_logging():

src/macta_tools/utils/requirements/__init__.py

@@ -0,0 +1,8 @@
+from macta_tools.utils.requirements._contains_requirement import ContainsRequirement
+from macta_tools.utils.requirements._equality_requirement import EqualityRequirement
+from macta_tools.utils.requirements._is_instance_requirement import IsInstanceRequirement
+from macta_tools.utils.requirements._not_none_requirement import NotNoneRequirement
+from macta_tools.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._requirement_list import RequirementList
+
+__all__ = ['Requirement', 'ContainsRequirement', 'IsInstanceRequirement', 'EqualityRequirement', 'RequirementList', 'NotNoneRequirement']

src/macta/utils/requirements/_contains_requirement.py → src/macta_tools/utils/requirements/_contains_requirement.py

@@ -2,7 +2,7 @@
 
 from pydantic import field_validator
 
-from macta.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._requirement import Requirement
 
 
 class ContainsRequirement(Requirement):

src/macta/utils/requirements/_equality_requirement.py → src/macta_tools/utils/requirements/_equality_requirement.py

@@ -1,6 +1,6 @@
 from typing import Any, cast
 
-from macta.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._requirement import Requirement
 
 
 class EqualityRequirement(Requirement):

src/macta/utils/requirements/_is_instance_requirement.py → src/macta_tools/utils/requirements/_is_instance_requirement.py

@@ -2,7 +2,7 @@
 
 from pydantic import field_validator
 
-from macta.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._requirement import Requirement
 
 
 class IsInstanceRequirement(Requirement):

src/macta/utils/requirements/_not_none_requirement.py → src/macta_tools/utils/requirements/_not_none_requirement.py

@@ -1,6 +1,6 @@
 from typing import Any, Optional
 
-from macta.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._requirement import Requirement
 
 
 class NotNoneRequirement(Requirement):

src/macta/utils/requirements/_requirement_list.py → src/macta_tools/utils/requirements/_requirement_list.py

@@ -3,8 +3,8 @@
 import pydantic
 from pydantic import field_validator
 
-from macta.utils.requirements._is_instance_requirement import IsInstanceRequirement
-from macta.utils.requirements._requirement import Requirement
+from macta_tools.utils.requirements._is_instance_requirement import IsInstanceRequirement
+from macta_tools.utils.requirements._requirement import Requirement
 
 
 # TODO: make this inherit from `dict` and use its methods to store data

tests/tools/test_celltypist.py

@@ -2,7 +2,7 @@
 
 # Skip this file if this module cannot be used with the current MACTA installation
 try:
-    from macta.tools import CelltypistInterface
+    from macta_tools.tools import CelltypistInterface
 except ImportError:
     pytest.skip(allow_module_level=True, reason='Celltypist-compatible extra not installed.')
 

tests/tools/test_scanvi.py

@@ -2,7 +2,7 @@
 
 # Skip this file if this module cannot be used with the current MACTA installation
 try:
-    from macta.tools import ScanviInterface
+    from macta_tools.tools import ScanviInterface
 except ImportError:
     pytest.skip(allow_module_level=True, reason='SCANVI-compatible extra not installed.')
 

tests/utils/requirements/test_contains_requirement.py

@@ -3,7 +3,7 @@
 
 import pytest
 
-from macta.utils.requirements import ContainsRequirement
+from macta_tools.utils.requirements import ContainsRequirement
 
 
 @pytest.mark.parametrize('collection, obj', [

tests/utils/requirements/test_is_instance_requirement.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from macta.utils.requirements import IsInstanceRequirement
+from macta_tools.utils.requirements import IsInstanceRequirement
 
 
 @pytest.mark.parametrize('obj_type, obj', [

tests/utils/requirements/test_requirement_list.py

@@ -1,4 +1,4 @@
-from macta.utils.requirements import EqualityRequirement, RequirementList
+from macta_tools.utils.requirements import EqualityRequirement, RequirementList
 
 
 def test_basic_rqlist() -> None:

tests/utils/requirements/test_some_requirement.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from macta.utils.requirements import NotNoneRequirement
+from macta_tools.utils.requirements import NotNoneRequirement
 
 
 def test_not_none_requirement_catches_none() -> None:

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 minversion = 4.0.0
-envlist = py38, py39, py310, torch38, flake8, isort, mypy
+envlist = py{38, 39, 310}, torch38, flake8, isort, mypy
 skip_missing_interpreters=True
 isolated_build = true