Merge pull request #135 from faridrashidi:develop

release v0.2.1

.github/workflows/ci.yml

@@ -87,14 +87,15 @@ jobs:
         -   name: Unit tests
             run: |
                 python -m pytest --cov=trisicell ./tests
-        -   name: Upload coverage
-            if: success()
-            env:
-                CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-            run: |
-                codecov --no-color --required --flags unittests
+        # -   name: Upload coverage
+        #     if: success()
+        #     env:
+        #         CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+        #     run: |
+        #         codecov --no-color --required --flags unittests
 
     codeql:
+        needs: lint
         name: code quality
         runs-on: ubuntu-latest
         permissions:

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+title: "Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity"
+message: "To cite Trisicell in publications, please cite it as below:"
+type: "article"
+authors:
+  - family-names: "Rashidi Mehrabadi"
+    given-names: "Farid"
+    orcid: "https://orcid.org/0000-0003-4103-4904"
+doi: "10.1101/2021.03.26.437185"
+url: "https://doi.org/10.1101/2021.03.26.437185"
+journal: "bioRxiv"
+year: "2021"

README.rst

@@ -57,7 +57,7 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :alt: Stars
 
 .. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=blue&logo=handshake&logoColor=FFFFFF&style=flat-square
-    :target: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.rst
+    :target: https://github.com/faridrashidi/trisicell/blob/master/CODE_OF_CONDUCT.rst
     :alt: Contributions Welcome
 
 .. |Compatible| image:: https://img.shields.io/pypi/pyversions/trisicell.svg?logo=python&logoColor=FFFFFF&style=flat-square&color=blue

docs/source/installation.rst

@@ -44,4 +44,4 @@ If you run into issues, do not hesitate to approach us or raise a
 .. _PyPI: https://pypi.org/project/trisicell
 .. _Github: https://github.com/faridrashidi/trisicell
 .. _`Github issue`: https://github.com/faridrashidi/trisicell/issues/new/choose
-.. _contributing guide: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.rst
+.. _contributing guide: https://github.com/faridrashidi/trisicell/blob/master/CODE_OF_CONDUCT.rst

requirements.txt

@@ -18,6 +18,7 @@ pybnb
 pydot
 python_sat
 pyyaml
+scanpy
 scikit_learn
 scipy
 seaborn

tests/test_datasets.py

@@ -26,57 +26,20 @@ def test_load_datasets(self):
         adata = tsc.datasets.test()
         assert adata.shape == (20, 20)
 
-        adata = tsc.datasets.sublines_bwes()
-        assert adata.shape == (24, 6653)
-        mdata = tsc.datasets.sublines_bwts()
-        assert mdata.shape == (33, 55937)
-        mdata = tsc.datasets.sublines_scrnaseq()
-        assert mdata.shape == (175, 55851)
-        mdata = tsc.datasets.treated_actla4()
-        assert mdata.shape == (508, 58710)
-        mdata = tsc.datasets.treated_igg_ss2()
-        assert mdata.shape == (163, 56854)
-        mdata = tsc.datasets.treated_igg_sw()
-        assert mdata.shape == (163, 56854)
+        # adata = tsc.datasets.sublines_bwes()
+        # assert adata.shape == (24, 6653)
+        # mdata = tsc.datasets.sublines_bwts()
+        # assert mdata.shape == (33, 55937)
+        # mdata = tsc.datasets.sublines_scrnaseq()
+        # assert mdata.shape == (175, 55851)
+        # mdata = tsc.datasets.treated_actla4()
+        # assert mdata.shape == (508, 58710)
+        # mdata = tsc.datasets.treated_igg_ss2()
+        # assert mdata.shape == (163, 56854)
+        # mdata = tsc.datasets.treated_igg_sw()
+        # assert mdata.shape == (163, 56854)
 
-        adata = tsc.datasets.acute_lymphocytic_leukemia1()
-        assert adata.shape == (111, 20)
-        adata = tsc.datasets.acute_lymphocytic_leukemia2()
-        assert adata.shape == (102, 16)
-        adata = tsc.datasets.acute_lymphocytic_leukemia3()
-        assert adata.shape == (150, 49)
-        adata = tsc.datasets.acute_lymphocytic_leukemia4()
-        assert adata.shape == (143, 78)
-        adata = tsc.datasets.acute_lymphocytic_leukemia5()
-        assert adata.shape == (96, 105)
-        adata = tsc.datasets.acute_lymphocytic_leukemia6()
-        assert adata.shape == (146, 10)
-        adata = tsc.datasets.colorectal1()
-        assert adata.shape == (178, 16)
         adata = tsc.datasets.colorectal2()
         assert adata.shape == (78, 25)
-        # adata = tsc.datasets.colorectal3()
-        adata = tsc.datasets.erbc()
-        assert adata.shape == (47, 40)
         adata = tsc.datasets.high_grade_serous_ovarian_cancer_3celllines()
         assert adata.shape == (891, 14068)
-        adata = tsc.datasets.melanoma20()
-        assert adata.shape == (20, 2367)
-        adata = tsc.datasets.muscle_invasive_bladder()
-        assert adata.shape == (44, 443)
-        adata = tsc.datasets.myeloproliferative_neoplasms18()
-        assert adata.shape == (58, 18)
-        adata = tsc.datasets.myeloproliferative_neoplasms78()
-        assert adata.shape == (58, 78)
-        adata = tsc.datasets.myeloproliferative_neoplasms712()
-        assert adata.shape == (58, 712)
-        adata = tsc.datasets.oligodendroglioma_idh_mutated_tumor()
-        assert adata.shape == (579, 77)
-        adata = tsc.datasets.renal_cell_carcinoma()
-        assert adata.shape == (17, 35)
-        adata = tsc.datasets.tnbc()
-        assert adata.shape == (16, 20)
-        # adata = tsc.datasets.high_grade_serous_ovarian_cancer1()
-        # adata = tsc.datasets.high_grade_serous_ovarian_cancer2()
-        # adata = tsc.datasets.high_grade_serous_ovarian_cancer3()
-        # adata = tsc.datasets.acute_lymphocytic_leukemia_many()

trisicell/datasets/__init__.py

@@ -1,64 +1,23 @@
 """Datasets Module."""
 
 from trisicell.datasets._datasets import (
-    acute_lymphocytic_leukemia1,
-    acute_lymphocytic_leukemia2,
-    acute_lymphocytic_leukemia3,
-    acute_lymphocytic_leukemia4,
-    acute_lymphocytic_leukemia5,
-    acute_lymphocytic_leukemia6,
-    colorectal1,
     colorectal2,
-    colorectal3,
-    erbc,
     example,
-    high_grade_serous_ovarian_cancer1,
-    high_grade_serous_ovarian_cancer2,
-    high_grade_serous_ovarian_cancer3,
     high_grade_serous_ovarian_cancer_3celllines,
-    melanoma20,
-    muscle_invasive_bladder,
-    myeloproliferative_neoplasms18,
-    myeloproliferative_neoplasms78,
-    myeloproliferative_neoplasms712,
-    oligodendroglioma_idh_mutated_tumor,
-    renal_cell_carcinoma,
     sublines_bwes,
     sublines_bwts,
     sublines_scrnaseq,
     test,
-    tnbc,
     treated_actla4,
     treated_igg_ss2,
     treated_igg_sw,
 )
 from trisicell.datasets._simulate import add_doublets, add_noise, simulate
 
 __all__ = (
-    acute_lymphocytic_leukemia1,
-    acute_lymphocytic_leukemia2,
-    acute_lymphocytic_leukemia3,
-    acute_lymphocytic_leukemia4,
-    acute_lymphocytic_leukemia5,
-    acute_lymphocytic_leukemia6,
-    colorectal1,
     colorectal2,
-    colorectal3,
-    erbc,
     example,
-    high_grade_serous_ovarian_cancer1,
-    high_grade_serous_ovarian_cancer2,
-    high_grade_serous_ovarian_cancer3,
     high_grade_serous_ovarian_cancer_3celllines,
-    melanoma20,
-    muscle_invasive_bladder,
-    myeloproliferative_neoplasms18,
-    myeloproliferative_neoplasms78,
-    myeloproliferative_neoplasms712,
-    oligodendroglioma_idh_mutated_tumor,
-    renal_cell_carcinoma,
-    test,
-    tnbc,
     simulate,
     add_noise,
     add_doublets,
@@ -68,4 +27,5 @@
     treated_actla4,
     treated_igg_ss2,
     treated_igg_sw,
+    test,
 )