release v0.0.12 (#28)

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.11
+current_version = 0.0.12
 commit = True
 tag = False
 files = setup.py trisicell/__init__.py

README.rst

@@ -1,5 +1,5 @@
-|DOI| |Stars| |PyPI| |PyPIDownloads| |Contributions Welcome| |Build Status|
-|Docs Status| |Pre-commit| |Code Score| |Code Style|
+|DOI| |Stars| |Compatible| |PyPI| |PyPiDownloads| |Contributions Welcome| |Build Status|
+|Docs Status| |Pre-commit| |Code Score| |License| |Code Style|
 
 
 Trisicell - |subst|
@@ -37,39 +37,47 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
 .. |subst| replace:: Scalable intratumor heterogeneity inference and validation
                     from single-cell data
 
-.. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2021.03.26.437185-orange?style=flat-square
+.. |DOI| image:: https://img.shields.io/badge/DOI-10.1101/2021.03.26.437185-orange?logo=gitbook&logoColor=FFFFFF&style=flat-square
     :target: https://doi.org/10.1101/2021.03.26.437185
     :alt: DOI
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/trisicell?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue
     :target: https://pypi.org/project/trisicell
     :alt: PyPI
 
-.. |PyPIDownloads| image:: https://img.shields.io/badge/dynamic/json?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ftrisicell
+.. |PyPyDownloads| image:: https://img.shields.io/badge/dynamic/json?logo=PyPi&logoColor=FFFFFF&style=flat-square&color=blue&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Ftrisicell
     :target: https://pepy.tech/project/trisicell
-    :alt: PyPIDownloads
+    :alt: PyPyDownloads
+
+.. |PyPiDownloads| image:: https://img.shields.io/pypi/dm/trisicell.svg?logo=docusign&logoColor=FFFFFF&style=flat-square&color=blue
+    :target: https://pepy.tech/project/trisicell
+    :alt: PyPiDownloads
 
 .. |Stars| image:: https://img.shields.io/github/stars/faridrashidi/trisicell?logo=GitHub&color=yellow&style=flat-square
     :target: https://github.com/faridrashidi/trisicell
     :alt: Stars
 
-.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=0059b3&style=flat-square
+.. |Contributions Welcome| image:: https://img.shields.io/static/v1.svg?label=contributions&message=welcome&color=0059b3&logo=handshake&logoColor=FFFFFF&style=flat-square
     :target: https://github.com/faridrashidi/trisicell/blob/master/CONTRIBUTING.rst
     :alt: Contributions Welcome
 
-.. |Build Status| image:: https://img.shields.io/github/workflow/status/faridrashidi/trisicell/CI/master?label=build&logo=github&style=flat-square
+.. |Compatible| image:: https://img.shields.io/pypi/pyversions/trisicell.svg?logo=python&logoColor=FFFFFF&style=flat-square&color=blue
+    :target: https://pypi.org/project/trisicell
+    :alt: Compatible
+
+.. |Build Status| image:: https://img.shields.io/github/workflow/status/faridrashidi/trisicell/CI/master?label=build&logo=githubactions&logoColor=FFFFFF&style=flat-square
     :target: https://github.com/faridrashidi/trisicell/actions?query=workflow%3ACI
     :alt: Build Status
 
-.. |Docs Status| image:: https://readthedocs.org/projects/trisicell/badge/?version=latest&style=flat-square
+.. |Docs Status| image:: https://img.shields.io/readthedocs/trisicell/latest?logo=readthedocs&logoColor=FFFFFF&style=flat-square
     :target: https://trisicell.readthedocs.io
     :alt: Docs Status
 
 .. |Pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=flat-square
     :target: https://github.com/pre-commit/pre-commit
     :alt: Pre-commit
 
-.. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square
+.. |Code Style| image:: https://img.shields.io/badge/code%20style-black-000000.svg?logo=visualstudiocode&logoColor=FFFFFF&style=flat-square
     :target: https://github.com/python/black
     :alt: Code Style
 
@@ -81,4 +89,9 @@ Trisicell was developed in collaboration between the `Cancer Data Science Labora
     :target: https://codecov.io/gh/faridrashidi/trisicell
     :alt: Codecov
 
+.. |License| image:: https://img.shields.io/pypi/l/trisicell.svg?logo=creativecommons&logoColor=FFFFFF&style=flat-square&color=blueviolet
+    :target: https://github.com/faridrashidi/trisicell/blob/master/LICENSE
+    :alt: License
+
+
 .. _preprint: https://doi.org/10.1101/2021.03.26.437185

setup.py

@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.0.11"
+    __version__ = "0.0.12"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"

trisicell/__init__.py

@@ -7,5 +7,5 @@
 __author__ = ", ".join(["Farid Rashidi"])
 __maintainer__ = ", ".join(["Farid Rashidi"])
 __email__ = ", ".join(["[email protected]"])
-__version__ = "0.0.11"
+__version__ = "0.0.12"
 __all__ = (datasets, io, logg, pl, pp, settings, tl, ul)

trisicell/commands/_phiscs.py

@@ -65,13 +65,21 @@ def phiscsb(genotype_file, alpha, beta):
 )
 @click.option(
     "--time_out",
-    "-to",
+    "-t",
     default=86400,
     type=int,
     show_default=True,
     help="Timelimit of the program.",
 )
-def phiscsi(genotype_file, alpha, beta, time_out):
+@click.option(
+    "--n_threads",
+    "-p",
+    default=1,
+    type=int,
+    show_default=True,
+    help="Number of threads.",
+)
+def phiscsi(genotype_file, alpha, beta, time_out, n_threads):
     """PhISCS-I.
 
     A combinatorial approach for subperfect
@@ -87,7 +95,9 @@ def phiscsi(genotype_file, alpha, beta, time_out):
     tsc.settings.logfile = f"{outfile}.phiscsi.log"
 
     df_in = tsc.io.read(genotype_file)
-    df_out = tsc.tl.phiscsi(df_in, alpha=alpha, beta=beta, time_out=time_out)
+    df_out = tsc.tl.phiscsi(
+        df_in, alpha=alpha, beta=beta, time_out=time_out, n_threads=n_threads
+    )
     tsc.io.write(df_out, f"{outfile}.phiscsi.CFMatrix")
 
     return None

trisicell/tl/solver/_phiscs.py

@@ -123,13 +123,14 @@ def phiscsb(df_input, alpha, beta, experiment=False):
     return df_output
 
 
-def phiscsi(df_input, alpha, beta, time_out=86400):
+def phiscsi(df_input, alpha, beta, time_out=86400, n_threads=1):
     gp, gp_is_not_imported = tsc.ul.import_gurobi()
     if gp_is_not_imported:
         tsc.logg.error("Unable to import a package!")
 
     tsc.logg.info(
-        f"running PhISCS-I with alpha={alpha}, beta={beta}, time_out={time_out}"
+        f"running PhISCS-I with alpha={alpha}, beta={beta}, time_out={time_out}, "
+        f"n_threads={n_threads}"
     )
     cells = list(df_input.index)
     snvs = list(df_input.columns)
@@ -140,7 +141,7 @@ def phiscsi(df_input, alpha, beta, time_out=86400):
     model = gp.Model("ILP")
     model.Params.OutputFlag = 0
     model.Params.LogFile = ""
-    model.Params.Threads = 1
+    model.Params.Threads = n_threads
     model.Params.TimeLimit = time_out
 
     num_cells = len(cells)

trisicell/tl/solver/booster/_subsamples.py

@@ -27,6 +27,9 @@ def subsampling(
     # )
     # tsc.logg.info(f"id,m,i0,i1,i3,o0,o1,f01,f10,f30,f31,r")
 
+    if solver.lower() == "scite":
+        time_out = n_iterations
+
     @tsc.ul.with_timeout(time_out)
     def run(i):
         if sample_on == "muts":