Merge pull request #64692 from costrouc/python-starfish-init

pythonPackages.starfish: init at 0.1.3

pkgs/development/python-modules/asciitree/default.nix

@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "asciitree";
+  version = "0.3.3";
+
+  src = fetchFromGitHub {
+    owner = "mbr";
+    repo = pname;
+    rev = version;
+    sha256 = "071wlpyi8pa262sj9xdy0zbj163z84dasxad363z3sfndqxw78h1";
+  };
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Draws ASCII trees";
+    homepage = https://github.com/mbr/asciitree;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/diskcache/default.nix

@@ -0,0 +1,26 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, tox
+}:
+
+buildPythonPackage rec {
+  pname = "diskcache";
+  version = "4.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "7c20b58ed07d03bbfba793f823d1fc27a61e590371fe6011fa1319a25c028cd1";
+  };
+
+  checkInputs = [
+    tox
+  ];
+
+  meta = with lib; {
+    description = "Disk and file backed persistent cache";
+    homepage = https://www.grantjenks.com/docs/diskcache/;
+    license = licenses.asl20;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/regional/default.nix

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, scipy
+, matplotlib
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "regional";
+  version = "1.1.2";
+
+  src = fetchFromGitHub {
+    owner = "freeman-lab";
+    repo = pname;
+    rev = "e3a29c58982e5cd3d5700131ac96e5e0b84fb981"; # no tags in repo
+    sha256 = "03qgm35q9sa5cy0kkw4bj60zfylw0isfzb96nlhdfrsigzs2zkxv";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    matplotlib
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Simple manipualtion and display of spatial regions";
+    homepage = https://github.com/freeman-lab/regional;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/showit/default.nix

@@ -0,0 +1,39 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, matplotlib
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "showit";
+  version = "1.1.4";
+
+  src = fetchFromGitHub {
+    owner = "freeman-lab";
+    repo = pname;
+    rev = "ef76425797c71fbe3795b4302c49ab5be6b0bacb"; # no tags in repo
+    sha256 = "0xd8isrlwwxlgji90lly1sq4l2a37rqvhsmyhv7bd3aj1dyjmdr6";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    matplotlib
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest test
+  '';
+
+  meta = with lib; {
+    description = "simple and sensible display of images";
+    homepage = https://github.com/freeman-lab/showit;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/slicedimage/default.nix

@@ -0,0 +1,50 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, boto3
+, diskcache
+, enum34
+, packaging
+, pathlib
+, numpy
+, requests
+, scikitimage
+, six
+, pytest
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "slicedimage";
+  version = "3.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "adab09457e22465f05998fdcf8ea14179185f8e780a4021526ba163dd476cd02";
+  };
+
+  propagatedBuildInputs = [
+    boto3
+    diskcache
+    packaging
+    numpy
+    requests
+    scikitimage
+    six
+  ] ++ lib.optionals isPy27 [ pathlib enum34 ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Library to access sliced imaging data";
+    homepage = https://github.com/spacetx/slicedimage;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/starfish/default.nix

@@ -0,0 +1,89 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, click
+, dataclasses
+, jsonschema
+, matplotlib
+, numpy
+, pandas
+, regional
+, semantic-version
+, scikitimage
+, scikitlearn
+, scipy
+, showit
+, slicedimage
+, sympy
+, tqdm
+, trackpy
+, validators
+, xarray
+, ipywidgets
+, pytest
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "starfish";
+  version = "0.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "19bec2a869affbca0a7e3fc0aee1b9978ff7f0f1a2a8551c2d4ae148a7ddc251";
+  };
+
+  propagatedBuildInputs = [
+    click
+    jsonschema
+    matplotlib
+    numpy
+    pandas
+    regional
+    semantic-version
+    scikitimage
+    scikitlearn
+    scipy
+    showit
+    slicedimage
+    sympy
+    tqdm
+    trackpy
+    validators
+    xarray
+    ipywidgets
+    ] ++ lib.optionals (pythonOlder "3.7") [ dataclasses ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  postConfigure = ''
+    substituteInPlace REQUIREMENTS.txt \
+      --replace "slicedimage==3.1.1" "slicedimage"
+  '';
+
+  checkPhase = ''
+    # a few tests < 5% require
+    rm -rf starfish/test/full_pipelines/*
+    pytest starfish \
+      --ignore starfish/core/config/test/test_config.py \
+      --ignore starfish/core/experiment/builder/test/test_build.py \
+      --ignore starfish/core/experiment/test/test_experiment.py \
+      --ignore starfish/core/image/_filter/test/test_reduce.py \
+      --ignore starfish/core/image/_registration/_apply_transform/test/test_warp.py \
+      --ignore starfish/core/image/_registration/_learn_transform/test/test_translation.py \
+      --ignore starfish/core/image/_registration/test/test_transforms_list.py \
+      --ignore starfish/core/imagestack/test/test_max_proj.py \
+      --ignore starfish/core/recipe/test/test_recipe.py \
+      --ignore starfish/core/recipe/test/test_runnable.py \
+      --ignore starfish/core/test/test_profiler.py
+  '';
+
+  meta = with lib; {
+    description = "Pipelines and pipeline components for the analysis of image-based transcriptomics data";
+    homepage = https://spacetx-starfish.readthedocs.io/en/latest/;
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/trackpy/default.nix

@@ -0,0 +1,57 @@
+{ stdenv
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, scipy
+, six
+, pandas
+, pyyaml
+, matplotlib
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "trackpy";
+  version = "0.4.1";
+
+  src = fetchFromGitHub {
+    owner = "soft-matter";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "01fdv93f6z16gypmvqnlbjmcih7dmr7a63n5w9swmp11x3if4iyq";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    six
+    pandas
+    pyyaml
+    matplotlib
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    ${stdenv.lib.optionalString (stdenv.isDarwin) ''
+    # specifically needed for darwin
+    export HOME=$(mktemp -d)
+    mkdir -p $HOME/.matplotlib
+    echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
+    ''}
+
+    pytest trackpy --ignore trackpy/tests/test_motion.py \
+                   --ignore trackpy/tests/test_feature_saving.py \
+                   --ignore trackpy/tests/test_feature.py \
+                   --ignore trackpy/tests/test_legacy_linking.py
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Particle-tracking toolkit";
+    homepage = https://github.com/soft-matter/trackpy;
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/validators/default.nix

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+, decorator
+, pytest
+, isort
+, flake8
+}:
+
+buildPythonPackage rec {
+  pname = "validators";
+  version = "0.13.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "ea9bf8bf22aa692c205e12830d90b3b93950e5122d22bed9eb2f2fece0bba298";
+  };
+
+  propagatedBuildInputs = [
+    six
+    decorator
+  ];
+
+  checkInputs = [
+    pytest
+    flake8
+    isort
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Python Data Validation for Humans™";
+    homepage = https://github.com/kvesteri/validators;
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -177,6 +177,8 @@ in {
 
   asciimatics = callPackage ../development/python-modules/asciimatics { };
 
+  asciitree = callPackage ../development/python-modules/asciitree { };
+
   ase = callPackage ../development/python-modules/ase { };
 
   asn1crypto = callPackage ../development/python-modules/asn1crypto { };
@@ -957,6 +959,8 @@ in {
 
   slackclient = callPackage ../development/python-modules/slackclient { };
 
+  slicedimage = callPackage ../development/python-modules/slicedimage { };
+
   slicerator = callPackage ../development/python-modules/slicerator { };
 
   slither-analyzer = callPackage ../development/python-modules/slither-analyzer { };
@@ -2459,6 +2463,8 @@ in {
 
   regex = callPackage ../development/python-modules/regex { };
 
+  regional = callPackage ../development/python-modules/regional { };
+
   ratelimiter = callPackage ../development/python-modules/ratelimiter { };
 
   pywatchman = callPackage ../development/python-modules/pywatchman { };
@@ -2493,6 +2499,8 @@ in {
 
   statsd = callPackage ../development/python-modules/statsd { };
 
+  starfish = callPackage ../development/python-modules/starfish { };
+
   multi_key_dict = callPackage ../development/python-modules/multi_key_dict { };
 
   random2 = callPackage ../development/python-modules/random2 { };
@@ -2511,6 +2519,8 @@ in {
 
   zope_deprecation = callPackage ../development/python-modules/zope_deprecation { };
 
+  validators = callPackage ../development/python-modules/validators { };
+
   validictory = callPackage ../development/python-modules/validictory { };
 
   validate-email = callPackage ../development/python-modules/validate-email { };
@@ -4459,6 +4469,8 @@ in {
 
   should-dsl = callPackage ../development/python-modules/should-dsl { };
 
+  showit = callPackage ../development/python-modules/showit { };
+
   simplejson = callPackage ../development/python-modules/simplejson { };
 
   simplekml = callPackage ../development/python-modules/simplekml { };
@@ -4978,6 +4990,8 @@ in {
 
   traceback2 = callPackage ../development/python-modules/traceback2 { };
 
+  trackpy = callPackage ../development/python-modules/trackpy { };
+
   linecache2 = callPackage ../development/python-modules/linecache2 { };
 
   upass = callPackage ../development/python-modules/upass { };
@@ -5611,6 +5625,8 @@ in {
 
   node-semver = callPackage ../development/python-modules/node-semver { };
 
+  diskcache = callPackage ../development/python-modules/diskcache { };
+
   distro = callPackage ../development/python-modules/distro { };
 
   bz2file =  callPackage ../development/python-modules/bz2file { };