Merge pull request #24 from faridrashidi:release/v0.0.11

release v0.0.11
faridrashidi · Jul 4, 2021 · 70969a5 · 70969a5
2 parents 8ebf75e + 652adb5
commit 70969a5
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.10
+current_version = 0.0.11
 commit = True
 tag = False
 files = setup.py trisicell/__init__.py

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -145,7 +145,10 @@ jobs:
                 path: dist
 
         -   name: Publish wheels to PyPI
-            uses: pypa/gh-action-pypi-publish@v1.4.2
+            uses: pypa/gh-action-pypi-publish@master
             with:
                 user: __token__
                 password: ${{ secrets.PYPI_TOKEN }}
+                packages_dir: dist/artifact/
+                skip_existing: true
+                verbose: true
diff --git a/.scripts/ci/install.sh b/.scripts/ci/install.sh
@@ -5,9 +5,23 @@ set -ev
 echo "Installing APT dependencies"
 if [[ "$OS" == "macos-latest" ]]; then
   brew install R
+  # pip install rpy2>=3.3.0
+  # Rscript -e 'install.packages("devtools")'
+  # Rscript -e 'install.packages("BiocManager")'
+  # Rscript -e 'install.packages("tidyverse")'
+  # Rscript -e 'install.packages("cowplot")'
+  # Rscript -e 'devtools::install_github("YuLab-SMU/ggtree")'
+  # Rscript -e 'devtools::install_github("YuLab-SMU/aplot")'
+  # Rscript -e 'devtools::install_github("xiangpin/ggtreeExtra")'
+  # Rscript -e 'devtools::install_github("zhouzilu/DENDRO")'
+  # Rscript -e 'BiocManager::install("graph")'
+  # Rscript -e 'devtools::install_bitbucket("edith_ross/oncoNEM")'
+
   brew install graphviz
   pip install pygraphviz
+
   brew install graph-tool
+
   brew install mpich
   pip install mpi4py
 elif [[ "$OS" == "ubuntu-latest" ]]; then

diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
@@ -7,6 +7,16 @@ Release Notes
 =============
 
 
+Version 0.0.11 :small:`July 4, 2021`
+-------------------------------------
+
+This version includes:
+
+    - Fix some typos.
+    - Fix some bugs.
+    - Fix SCITE cythonizing issue.
+
+
 Version 0.0.10 :small:`July 3, 2021`
 -------------------------------------
 

diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.0.10"
+    __version__ = "0.0.11"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"
@@ -56,26 +56,26 @@
         extra_compile_args=["-O3", "-std=c++11", "-c"],
         language="c++",
     ),
-    # Extension(
-    #     "trisicell.external._scite",
-    #     sources=[
-    #         "trisicell/external/_scite.pyx",
-    #         "trisicell/external/scite/matrices.cpp",
-    #         "trisicell/external/scite/mcmcBinTreeMove.cpp",
-    #         "trisicell/external/scite/mcmc.cpp",
-    #         "trisicell/external/scite/mcmcTreeMove.cpp",
-    #         "trisicell/external/scite/output.cpp",
-    #         "trisicell/external/scite/rand.cpp",
-    #         "trisicell/external/scite/scoreBinTree.cpp",
-    #         "trisicell/external/scite/scoreTree.cpp",
-    #         "trisicell/external/scite/treelist.cpp",
-    #         "trisicell/external/scite/trees.cpp",
-    #         "trisicell/external/scite/findBestTrees.cpp",
-    #     ],
-    #     include_dirs=["trisicell/external/scite"],
-    #     extra_compile_args=["-std=c++11"],
-    #     language="c++",
-    # ),
+    Extension(
+        "trisicell.external._scite",
+        sources=[
+            "trisicell/external/_scite.pyx",
+            "trisicell/external/scite/matrices.cpp",
+            "trisicell/external/scite/mcmcBinTreeMove.cpp",
+            "trisicell/external/scite/mcmc.cpp",
+            "trisicell/external/scite/mcmcTreeMove.cpp",
+            "trisicell/external/scite/output.cpp",
+            "trisicell/external/scite/rand.cpp",
+            "trisicell/external/scite/scoreBinTree.cpp",
+            "trisicell/external/scite/scoreTree.cpp",
+            "trisicell/external/scite/treelist.cpp",
+            "trisicell/external/scite/trees.cpp",
+            "trisicell/external/scite/findBestTrees.cpp",
+        ],
+        include_dirs=["trisicell/external/scite"],
+        extra_compile_args=["-O3", "-std=c++11", "-c"],
+        language="c++",
+    ),
 ]
 
 
@@ -136,6 +136,7 @@ def no_cythonize(extensions, **_ignore):
     },
     platforms=["Linux", "MacOSX"],
     packages=find_packages(),
+    include_package_data=True,
     author=__author__,
     author_email=__email__,
     email=__email__,

diff --git a/tests/test_commands.py b/tests/test_commands.py
@@ -21,7 +21,6 @@ def test_scistree(self):
         )
         assert result.exit_code == 0
 
-    @pytest.mark.skip(reason="SCITE compilation issue!")
     def test_scite(self):
         runner = CliRunner()
         result = runner.invoke(
@@ -37,7 +36,6 @@ def test_scite(self):
         )
         assert result.exit_code == 0
 
-    @pytest.mark.skip(reason="SCITE compilation issue!")
     def test_scite_experiment(self):
         runner = CliRunner()
         result = runner.invoke(
@@ -68,7 +66,7 @@ def test_phiscsb(self):
         )
         assert result.exit_code == 0
 
-    @pytest.mark.skip(reason="PyTest issue with multithreading!")
+    @pytest.mark.skip(reason="PyTest issue with multithreading!")  # TODO:
     def test_booster(self):
         runner = CliRunner()
         result = runner.invoke(

diff --git a/tests/test_solvers.py b/tests/test_solvers.py
@@ -14,14 +14,13 @@ def test_simulate(self):
         is_cf = tsc.ul.is_conflict_free_gusfield(df_in)
         assert not is_cf
 
-    @pytest.mark.skip(reason="PyTest issue with redirecting the stdout!")
+    @pytest.mark.skip(reason="PyTest issue with redirecting the stdout!")  # TODO:
     def test_scistree(self):
         df_in = tsc.datasets.test()
         df_out = tsc.tl.scistree(df_in, alpha=0.0000001, beta=0.1)
         is_cf = tsc.ul.is_conflict_free_gusfield(df_out)
         assert is_cf
 
-    @pytest.mark.skip(reason="SCITE compilation issue!")
     def test_scite(self):
         df_in = tsc.datasets.test()
         df_out = tsc.tl.scite(
@@ -69,7 +68,7 @@ def test_phiscs_bulk(self):
         is_cf = tsc.ul.is_conflict_free_gusfield(df_out)
         assert is_cf
 
-    def test_booster(self):
+    def test_booster_phiscs(self):
         df_in = tsc.datasets.test()
         df_out = tsc.tl.booster(
             df_in,
@@ -81,6 +80,24 @@ def test_booster(self):
             n_samples=20,
             begin_index=0,
             n_jobs=1,
+            time_out=120,
+            dep_weight=5,
+        )
+        is_cf = tsc.ul.is_conflict_free_gusfield(df_out)
+        assert is_cf
+
+    def test_booster_scite(self):
+        df_in = tsc.datasets.test()
+        df_out = tsc.tl.booster(
+            df_in,
+            alpha=0.0000001,
+            beta=0.1,
+            solver="SCITE",
+            sample_on="muts",
+            sample_size=10,
+            n_samples=20,
+            begin_index=0,
+            n_jobs=1,
             n_iterations=10000,
             dep_weight=5,
         )

diff --git a/trisicell/__init__.py b/trisicell/__init__.py
@@ -7,5 +7,5 @@
 __author__ = ", ".join(["Farid Rashidi"])
 __maintainer__ = ", ".join(["Farid Rashidi"])
 __email__ = ", ".join(["[email protected]"])
-__version__ = "0.0.10"
+__version__ = "0.0.11"
 __all__ = (datasets, io, logg, pl, pp, settings, tl, ul)
diff --git a/trisicell/datasets/_datasets.py b/trisicell/datasets/_datasets.py
@@ -17,11 +17,6 @@ def example(kind):
     -------
     :class:`anndata.AnnData`
         An object that cells are in `.obs` and mutations are in `.var`.
-
-    Raises
-    ------
-    ValueError
-        If `kind` is not `genotype` or `expression`.
     """
 
     if kind.lower() == "genotype":
@@ -31,7 +26,7 @@ def example(kind):
             tsc.ul.get_file("trisicell.datasets/data/expression.h5ad.gz")
         )
     else:
-        raise ValueError("kind must be either genotype or expression")
+        tsc.logg.error("kind must be either genotype or expression")
 
 
 def test():

diff --git a/trisicell/datasets/_simulate.py b/trisicell/datasets/_simulate.py
@@ -38,7 +38,7 @@ def simulate(n_cells=10, n_muts=10, n_clones=3, alpha=0.00001, beta=0.1, missing
         "BiocManager::install('graph')\ndevtools::install_bitbucket('edith_ross/oncoNEM')\n",
     )
     if onconem_is_not_imported:
-        raise RuntimeError("Unable to import a package!")
+        tsc.logg.error("Unable to import a package!")
 
     import rpy2.robjects as ro
     from rpy2.robjects import pandas2ri
@@ -73,7 +73,7 @@ def splatter(noisy, ground, seed=5):
         "BiocManager::install('splatter')\n",
     )
     if splatter_is_not_imported:
-        raise RuntimeError("Unable to import a package!")
+        tsc.logg.error("Unable to import a package!")
 
     import rpy2.robjects as ro
 
@@ -166,7 +166,7 @@ def create_splatter():
         "BiocManager::install('splatter')\n",
     )
     if splatter_is_not_imported:
-        raise RuntimeError("Unable to import a package!")
+        tsc.logg.error("Unable to import a package!")
 
     import rpy2.robjects as ro
 

diff --git a/trisicell/external/bin/scite b/trisicell/external/bin/scite
diff --git a/trisicell/external/scite/findBestTrees.cpp b/trisicell/external/scite/findBestTrees.cpp
@@ -53,7 +53,7 @@ int m;                // number of samples
 char scoreType = 'm';
 int rep;            // number of repetitions of the MCMC
 int loops;          // number of loops within a MCMC
-double gamma = 1;
+double gammaParam = 1;
 double fd;          // rate of false discoveries (false positives 0->1)
 double ad1;          // rate of allelic dropout (false negatives 1->0)
 double ad2 = 0.0;         // rate of allelic dropout (2->1)
@@ -105,7 +105,7 @@ int main_in_c(int argc, char **argv)
 	if(trueTreeComp==true){ trueParentVec = getParentVectorFromGVfile(trueTreeFileName, n); }
 
 	/**  Find best scoring trees by MCMC  **/
-	sampleOutput = runMCMCbeta(optimalTrees, errorRates, rep, loops, gamma, moveProbs, n, m, dataMatrix, scoreType, trueParentVec, sampleStep, sample, chi, priorSd, useTreeList, treeType);
+	sampleOutput = runMCMCbeta(optimalTrees, errorRates, rep, loops, gammaParam, moveProbs, n, m, dataMatrix, scoreType, trueParentVec, sampleStep, sample, chi, priorSd, useTreeList, treeType);
 
 
 	/***  output results  ***/
@@ -274,7 +274,7 @@ int readParameters(int argc, char* argv[]){
 		} else if(strcmp(argv[i], "-l")==0) {
 			if (i + 1 < argc) { loops = atoi(argv[++i]);}
 		} else if(strcmp(argv[i], "-g")==0) {
-			if (i + 1 < argc) { gamma = atof(argv[++i]);}
+			if (i + 1 < argc) { gammaParam = atof(argv[++i]);}
 		} else if(strcmp(argv[i], "-fd")==0) {
 			if (i + 1 < argc) { fd = atof(argv[++i]);}
 		} else if(strcmp(argv[i],"-ad")==0) {

diff --git a/trisicell/io/_genotype.py b/trisicell/io/_genotype.py
@@ -26,23 +26,18 @@ def read(filepath):
     -------
     :class:`pandas.DataFrame` or :class:`anndata.AnnData`
         Depends on the format of the input file the output type is different.
-
-    Raises
-    ------
-    ValueError
-        If the extension is not one of the above.
     """
 
     ext = os.path.splitext(filepath)[-1]
     if ext in [".SC", ".CFMatrix", ".before_FP_FN_NA", ".tsv"]:
         sc = pd.read_table(filepath, index_col=0)
         if len(sc.columns) != len(set(sc.columns)):
-            raise RuntimeError("Mutation ids must be unique!")
+            tsc.logg.error("Mutation ids must be unique!")
         return sc
     elif ext in [".h5ad", ".gz"]:
         return ad.read(filepath)
     else:
-        raise ValueError("Extension is wrong!")
+        tsc.logg.error("Extension is wrong!")
 
 
 def write(obj, filepath):
@@ -54,13 +49,6 @@ def write(obj, filepath):
         The input object which is going to be written in a file.
     filepath : :obj:`str`
         The file path where the `obj` must be written in.
-
-    Raises
-    ------
-    ValueError
-        If `obj` is not an instance of:
-            :class:`pandas.DataFrame`
-            :class:`anndata.AnnData`
     """
 
     if isinstance(obj, pd.DataFrame):
@@ -69,7 +57,7 @@ def write(obj, filepath):
     elif isinstance(obj, ad.AnnData):
         obj.write(filepath + ".h5ad.gz", compression="gzip")
     else:
-        raise ValueError("Object instance is wrong!")
+        tsc.logg.error("Object instance is wrong!")
 
 
 def read_gatk(

diff --git a/trisicell/logging/_logging.py b/trisicell/logging/_logging.py
@@ -18,7 +18,7 @@ def info(*args, **kwargs):
     [type]
         [description]
     """
-    return msg(*args, v="info", **kwargs)
+    msg(*args, v="info", **kwargs)
 
 
 def error(*args, **kwargs):
@@ -30,7 +30,8 @@ def error(*args, **kwargs):
         [description]
     """
     args = ("Error:",) + args
-    return msg(*args, v="error", **kwargs)
+    msg(*args, v="error", **kwargs)
+    exit(1)
 
 
 def warn(*args, **kwargs):
@@ -42,7 +43,7 @@ def warn(*args, **kwargs):
         [description]
     """
     args = ("WARNING:",) + args
-    return msg(*args, v="warn", **kwargs)
+    msg(*args, v="warn", **kwargs)
 
 
 def hint(*args, **kwargs):
@@ -53,7 +54,7 @@ def hint(*args, **kwargs):
     [type]
         [description]
     """
-    return msg(*args, v="hint", **kwargs)
+    msg(*args, v="hint", **kwargs)
 
 
 def debug(*args, **kwargs):
@@ -65,7 +66,7 @@ def debug(*args, **kwargs):
         [description]
     """
     args = ("DEBUG:",) + args
-    return msg(*args, v="debug", **kwargs)
+    msg(*args, v="debug", **kwargs)
 
 
 def msg(*msg, v, time=False, end="\n"):