Merge pull request #124 from faridrashidi/develop

release v0.2.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.1
+current_version = 0.2.0
 commit = True
 message = [skip ci] {current_version} → {new_version}
 tag = False

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
         outputs:
             skip: ${{ steps.ci-skip-step.outputs.ci-skip }}
         steps:
-        -   uses: actions/checkout@v2
+        -   uses: actions/checkout@v3
             with:
                 fetch-depth: 0
         -   id: ci-skip-step
@@ -35,7 +35,7 @@ jobs:
         if: ${{ github.event_name == 'schedule' || needs.init.outputs.skip == 'false' }}
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v2
+        -   uses: actions/checkout@v3
         -   name: Set up Python 3.7
             uses: actions/setup-python@v2
             with:
@@ -63,7 +63,7 @@ jobs:
             PYTHON: ${{ matrix.python }}
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         steps:
-        -   uses: actions/checkout@v2
+        -   uses: actions/checkout@v3
             with:
                 fetch-depth: 0
         -   name: Set up Python ${{ matrix.python }}
@@ -121,6 +121,8 @@ jobs:
                 category: "/language:${{ matrix.language }}"
 
     build_wheels:
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        needs: test
         name: build wheels on ${{ matrix.os }}
         runs-on: ${{ matrix.os }}
         strategy:
@@ -129,9 +131,9 @@ jobs:
             matrix:
                 os: [ubuntu-latest, macos-latest]
         steps:
-        -   uses: actions/checkout@v2
+        -   uses: actions/checkout@v3
         -   name: Install Python
-            uses: actions/setup-python@v2
+            uses: actions/setup-python@v4
             with:
                 python-version: '3.8'
         -   name: Build wheels
@@ -141,12 +143,14 @@ jobs:
                 path: ./wheelhouse/*.whl
 
     build_sdist:
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        needs: build_wheels
         name: build source distribution
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v2
+        -   uses: actions/checkout@v3
         -   name: Install Python
-            uses: actions/setup-python@v2
+            uses: actions/setup-python@v4
             with:
                 python-version: '3.8'
         -   name: Build sdist

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Farid Rashidi
+Copyright (c) 2021-2023, Farid Rashidi
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

docs/source/api.rst

@@ -111,4 +111,5 @@ This module offers a bunch of functions for simulating data.
 
     datasets.example
     datasets.sublines_bwes
+    datasets.sublines_bwts
     datasets.sublines_scrnaseq

docs/source/conf.py

@@ -45,7 +45,7 @@
 title = (
     "Scalable intratumor heterogeneity inference and validation from single-cell data"
 )
-copyright = f"2021-2022, {author}"
+copyright = f"2021-2023, {author}"
 release = "master"
 version = f"master ({trisicell.__version__})"
 

docs/source/release_notes.rst

@@ -7,13 +7,12 @@ Release Notes
 =============
 
 
-Version 0.1.0 :small:`June 24, 2022`
-------------------------------------
+Version 0.1.1 :small:`December 28, 2022`
+----------------------------------------
 
 This version includes:
 
-    - Add sublines bWES dataset.
-    - Add sublines scRNAseq dataset.
+    - Fix the bug of CI.
 
 
 Version 0.0.21 :small:`April 22, 2022`

setup.cfg

@@ -22,6 +22,7 @@ ignore =
     B020, # B020 Found for loop that reassigns the iterable it is iterating with each
     B902, # B902 blind except Exception: statement
     C400, # C400 Unnecessary generator - rewrite as a list comprehension
+    E203, # E203 whitespace before ':'
 [tool:pytest]
 filterwarnings = ignore::DeprecationWarning
 [coverage:run]

setup.py

@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.1.1"
+    __version__ = "0.2.0"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"
@@ -185,6 +185,7 @@ def no_cythonize(extensions, **_ignore):
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Visualization",
     ],

trisicell/__init__.py

@@ -7,5 +7,5 @@
 __author__ = ", ".join(["Farid Rashidi"])
 __maintainer__ = ", ".join(["Farid Rashidi"])
 __email__ = ", ".join(["[email protected]"])
-__version__ = "0.1.1"
+__version__ = "0.2.0"
 __all__ = (datasets, io, logg, pl, pp, settings, tl, ul)

trisicell/commands/_trees.py

@@ -15,7 +15,7 @@
     ),
 )
 def cf2newick(cf_file):
-    """"""
+    """CF2Newick."""
 
     outfile = os.path.splitext(cf_file)[0]
     cf = tsc.io.read(cf_file)
@@ -37,7 +37,7 @@ def cf2newick(cf_file):
     ),
 )
 def cf2tree(cf_file):
-    """"""
+    """CF2Tree."""
 
     outfile = os.path.splitext(cf_file)[0]
     cf = tsc.io.read(cf_file)

trisicell/datasets/__init__.py

@@ -24,6 +24,7 @@
     oligodendroglioma_idh_mutated_tumor,
     renal_cell_carcinoma,
     sublines_bwes,
+    sublines_bwts,
     sublines_scrnaseq,
     test,
     tnbc,
@@ -60,4 +61,5 @@
     add_doublets,
     sublines_bwes,
     sublines_scrnaseq,
+    sublines_bwts,
 )

trisicell/datasets/_datasets.py

@@ -31,6 +31,7 @@ def sublines_scrnaseq():
     See Also
     --------
     :func:`trisicell.datasets.sublines_bwes`.
+    :func:`trisicell.datasets.sublines_bwts`.
     """
 
     mdata = md.read_h5mu(
@@ -69,13 +70,51 @@ def sublines_bwes():
     See Also
     --------
     :func:`trisicell.datasets.sublines_scrnaseq`.
+    :func:`trisicell.datasets.sublines_bwts`.
     """
     adata = tsc.io.read(
         tsc.ul.get_file("trisicell.datasets/data/sublines_bwes.h5ad.gz")
     )
     return adata
 
 
+def sublines_bwts():
+    """Trisicell sublines bWTS data.
+
+    The size is n_cells × n_muts = 33 × 536
+
+    Returns
+    -------
+    :class:`mudata.MuData`
+
+        A mudata with two modalities (`.mod`)
+
+    Examples
+    --------
+    >>> mdata = tsc.datasets.sublines_bwts()
+    >>> mdata
+    MuData object with n_obs × n_vars = 33 × 55851
+    2 modalities
+      expression: 175 x 55401
+        obs:	'cells', 'uniquely_mapped_percent', 'num_splices', ...
+        layers:	'fpkm', 'tpm'
+      mutation:	33 x 536
+        obs:	'cells', 'clone', 'mps', 'zscore', 'group', 'Axl', 'Mitf', 'day', ...
+        var:	'kind', 'amino_acid_change', 'ensemble', 'gene', 'chrom', 'position',...
+        layers:	'genotype', 'mutant', 'total', 'trisicell_input', 'trisicell_output'
+
+    See Also
+    --------
+    :func:`trisicell.datasets.sublines_bwes`.
+    :func:`trisicell.datasets.sublines_scrnaseq`.
+    """
+
+    mdata = md.read_h5mu(
+        tsc.ul.get_file("trisicell.datasets/data/sublines_bwts.h5md.gz")
+    )
+    return mdata
+
+
 def example(is_expression=False):
     """Return an example for sanity checking and playing with Trisicell.
 

trisicell/tl/solver/_bnb.py

@@ -466,8 +466,8 @@ def make_constraints_np_matrix(
                         x = np.empty((r01.shape[0] + r10.shape[0], 2), dtype=np.int)
                         x[: len(r01), 0] = r01
                         x[: len(r01), 1] = p
-                        x[-len(r10) :, 0] = r10  # noqa
-                        x[-len(r10) :, 1] = q  # noqa
+                        x[-len(r10) :, 0] = r10
+                        x[-len(r10) :, 1] = q
 
                         for a, b, ind in itertools.product(r01, r10, range(x.shape[0])):
                             for row, col in [

trisicell/tl/solver/booster/_reconstruct_big_tree.py

@@ -34,13 +34,13 @@ def read_matrix_from_file_into_hash(path_matrix_file):
     assert len(input_lines) > 0, "ERROR. Input file " + path_matrix_file + " is empty."
 
     header_entries = input_lines[0].strip().split()
-    column_ids = header_entries[1 : len(header_entries)]  # noqa
+    column_ids = header_entries[1 : len(header_entries)]
     num_columns = len(column_ids)
     assert num_columns != 0, (
         "ERROR. Number of columns in " + path_matrix_file + " equals zero. Exiting!!!"
     )
 
-    input_lines_without_header = input_lines[1 : len(input_lines)]  # noqa
+    input_lines_without_header = input_lines[1 : len(input_lines)]
     D = {}
     for line in input_lines_without_header:
         line_columns = line.strip().split()