Merge pull request #8 from lldelisle/switch_pyprojecttoml

Switch pyprojecttoml

.github/workflows/python-publish.yml

@@ -22,22 +22,21 @@ jobs:
 
     runs-on: ubuntu-latest
 
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
     steps:
     - uses: actions/checkout@v3
-    - uses: mamba-org/setup-micromamba@main
+    - name: Set up Python
+      uses: actions/setup-python@v3
       with:
-        environment-file: ./baredSC_dev_env.yml
-        cache-downloads: true
-        environment-name: baredSC_dev
-    - name: pip install
+        python-version: '3.10'
+    - name: Install dependencies
       run: |
-        micromamba activate baredSC_dev
+        python -m pip install --upgrade pip
         pip install build
-        pip install .
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_BAREDSC_API_TOKEN }}
+      uses: pypa/[email protected]

.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/__init__.py

@@ -5,5 +5,3 @@
 on the probability density function (PDF) of expression of one or two genes
 from single-cell RNA-seq data. It uses the raw counts and the total number of UMI for each cell.
 """
-
-from . _version import __version__

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

@@ -7,6 +7,7 @@
 import time
 from tempfile import NamedTemporaryFile
 from shutil import copy
+from importlib.metadata import version
 import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
@@ -16,8 +17,6 @@
 import anndata
 from samsam import acf
 
-from . _version import __version__
-
 mpl.use('agg')
 
 
@@ -388,7 +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"
@@ -592,7 +591,7 @@ def parse_arguments(tool: str) -> argparse.ArgumentParser:
                             help="Size of sampling of random parameters in logevidence evaluation.")
   # Version
   argp.add_argument('--version', action='version',
-                    version=__version__)
+                    version=version('baredSC'))
   return argp
 
 

baredSC/tests/test_baredSC_1d.py

@@ -21,7 +21,7 @@
 
 BARED_1D_TEXT_SUFFIX = ['_neff.txt', '_p.txt', '_pdf.txt', '_posterior_per_cell.txt']
 
-TOLERENCE = 18  # default matplotlib pixed difference tolerance
+TOLERENCE = 13  # default matplotlib pixed difference tolerance
 
 
 def test_baredSC_1d_1gauss_default():

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,

baredSC/tests/test_data/2d_small_2gauss_corr.txt

@@ -1,2 +1,2 @@
 mean	median	low	high	pval	error
-0.902971588834658	0.9030205591240211	0.8808479278110088	0.9249439927709214	0.007859609399117668	0.007859609399117668
+0.9029716395251455	0.9030200651684039	0.8808479278441326	0.9249441195524556	0.007859623867374954	0.007859623867374954

baredSC/tests/test_data/2d_small_2gauss_neff.txt

@@ -1 +1 @@
-127.23278590819812
+127.23255169384986

baredSC/tests/test_data/2d_small_2gauss_p.txt

@@ -1,12 +1,12 @@
 name	low	median	high
-xy_mux0	0.3421735749355604	0.36400142067277885	0.38414407467979367
-xy_muy0	0.3602753667616778	0.3797834812619477	0.3997083085113705
-xy_scalex0	0.128373484740148	0.13754306887169315	0.154475100117708
-xy_scaley0	0.11267797849970684	0.13404387324572375	0.1636497454683696
-xy_corr0	-0.056936609709389754	0.20134274953150133	0.4823245136404016
-xy_amp1	0.4683630960583824	0.4935067017747425	0.5184297378623833
-xy_mux1	0.9950898144773097	1.0128387895441175	1.0323483080264237
-xy_muy1	0.9882799141570242	1.0073935336038764	1.0262810747590292
-xy_scalex1	0.12680233831791496	0.1317913482460104	0.1439711554909536
-xy_scaley1	0.10695025120288884	0.11525119819932761	0.13138587521715606
-xy_corr1	0.27825576244514594	0.5311286235242539	0.7541979912185461
+xy_mux0	0.3421738328109765	0.36400189932266336	0.3841440747553726
+xy_muy0	0.3602753667866474	0.3797834812932726	0.39970830854564193
+xy_scalex0	0.12837392956595675	0.13754306888676632	0.1544751002101545
+xy_scaley0	0.11267797846698233	0.1340437185508837	0.16364975095169854
+xy_corr0	-0.05693660975737857	0.20134265783169808	0.4823245134294125
+xy_amp1	0.4683630960248498	0.49350668946491333	0.5184297378980278
+xy_mux1	0.9950898816264488	1.012838789457257	1.0323483079969673
+xy_muy1	0.9882799141741364	1.0073935335689348	1.0262810747408535
+xy_scalex1	0.12680170616971262	0.13179069883831943	0.14397113027517466
+xy_scaley1	0.1069508246498268	0.11525151370549018	0.13138555730081636
+xy_corr1	0.27825576227578863	0.5311286284596629	0.7541981226602934