diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c6c3e43116019cef78112485caa390bb9d7a1700..930ad63dd0baba9eb75f2fdd88e978ffa1963919 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,14 +14,15 @@ test-python:
script:
- apt-get update && apt install -y libblas-dev liblapack-dev python3-dev
- pip install -r requirements.txt
- - python setup.py test
+ - python -m unittest
+# - python setup.py test
parallel:
matrix:
- PYTHON_VERSION: [
# '3.7', # EOL
'3.8', # oldest
'3.10', # used in Dockerfile
- '3.12', # latest
+ '3.12',
]
@@ -127,7 +128,7 @@ build-backend:
-v $(pwd)/.eggs:/code/.eggs
-v $(pwd)/jass.egg-info:/code/jass.egg-info
"$CI_REGISTRY_IMAGE/$CI_COMMIT_REF_SLUG/${PATH_TAG}:$CI_COMMIT_SHA"
- python setup.py test
+ python -m unittest
build-client-dev:
diff --git a/chart/pvc-shared-data.yaml b/chart/pvc-shared-data.yaml
index 38c0a14f6448ff1c58970f112e25ebd4105fd0d5..fe918824548f2ca3390e23e9d5cf80a6c1a22958 100644
--- a/chart/pvc-shared-data.yaml
+++ b/chart/pvc-shared-data.yaml
@@ -8,5 +8,5 @@ spec:
resources:
requests:
storage: 80Gi
- storageClassName: isilon
+ storageClassName: ceph-fs
status: {}
\ No newline at end of file
diff --git a/chart/values.yaml b/chart/values.yaml
index 66caaed646d0eb59b4e19e14d5fa7067ef5ffb80..87acacf3ec131857ae3743ea0b00d3b16f3419ea 100644
--- a/chart/values.yaml
+++ b/chart/values.yaml
@@ -32,8 +32,9 @@ serviceAccount:
podAnnotations: {}
podSecurityContext:
- {}
- # fsGroup: 1001
+ runAsUser: 1000
+ runAsGroup: 1000
+ fsGroup: 1000
securityContext:
runAsNonRoot: true
@@ -85,7 +86,7 @@ backCronTasks:
projects:
size: 19Gi
minSizeToKeepFree: 10240 # size is in MB
- storageClassName: isilon
+ storageClassName: ceph-fs
client:
securityContext:
diff --git a/jass/models/plots.py b/jass/models/plots.py
index 3953d0f3419db0e4bbebd31e675a7d54a0be2991..ef60219ef9e54f91a5016d74d3c6851f78f69a2d 100644
--- a/jass/models/plots.py
+++ b/jass/models/plots.py
@@ -17,10 +17,10 @@ from matplotlib import colors
import matplotlib.patches as mpatches
from scipy.stats import norm, chi2
import seaborn as sns
-import os
from pandas import DataFrame, read_hdf
import pandas as pd
+default_chunk_size=50
def replaceZeroes(df):
"""
@@ -32,30 +32,34 @@ def replaceZeroes(df):
df.values[df.values == 0] = min_nonzero
return df
-def create_global_plot(work_file_path: str, global_plot_path: str):
+
+def get_info_4_global_plot(work_file_path: str):
+ regions = read_hdf(work_file_path, "Regions",columns=['Region','CHR','MiddlePosition'])
+ print(regions.dtypes)
+ N_reg = regions.Region.max() # Keep biggest element in Region column
+ binf = regions.Region.iloc[0]
+ chr_considered = regions.CHR.unique()
+ length_chr = regions.groupby("CHR").MiddlePosition.max() / 10 ** 6
+ length_chr.loc[0] = 0
+ return N_reg,binf,chr_considered,length_chr
+
+def create_global_plot(work_file_path: str, global_plot_path: str, chunk_size:int =default_chunk_size):
"""
create_global_plot
generate genome-wide manhattan plot for a given set of phenotypes
"""
- regions = read_hdf(work_file_path, "Regions")
- chr_length = regions.groupby('CHR').max().position
- N_reg= regions.Region.max()
+ N_reg,binf,chr_considered,length_chr=get_info_4_global_plot(work_file_path)
maxy = 0
fig = plt.figure(figsize=(30, 12))
ax = fig.add_subplot(111)
- chunk_size = 50
colors = [
'#4287f5',
'orangered'
]
- binf=regions.Region.iloc[0]
- bsup= binf+chunk_size
- chr_considered= regions.CHR.unique()
- length_chr = regions.groupby("CHR").MiddlePosition.max() / 10**6
- length_chr.loc[0] = 0
+
label = "Chr"+length_chr.loc[chr_considered].index.astype("str")
lab_pos = length_chr.loc[chr_considered]/2
@@ -63,7 +67,7 @@ def create_global_plot(work_file_path: str, global_plot_path: str):
pos_shift.index = pos_shift.index +1
pos_shift.loc[chr_considered[0]] = 0
lab_pos = lab_pos + [pos_shift.loc[i] for i in chr_considered]
-
+ bsup = binf + chunk_size
while binf < N_reg:
df = read_hdf(work_file_path, "SumStatTab", columns=["CHR","position", 'JASS_PVAL', "Region"], where = "Region >= {0} and Region < {1}".format(binf, bsup))
binf+= chunk_size
diff --git a/jass/test/expected_graphs/expected_global_plot.png b/jass/test/expected_graphs/expected_global_plot.png
new file mode 100644
index 0000000000000000000000000000000000000000..a1896d6c7795ac13c1aa6e542cf41f7246e43a08
Binary files /dev/null and b/jass/test/expected_graphs/expected_global_plot.png differ
diff --git a/jass/test/test_plots.py b/jass/test/test_plots.py
index ad0012abe26c219928e091f836c1a26e87034b9f..99d12721b4baa6fe3789b16b8d06b819ce360235 100644
--- a/jass/test/test_plots.py
+++ b/jass/test/test_plots.py
@@ -3,8 +3,10 @@
from __future__ import absolute_import
import os, shutil, tempfile
from pathlib import Path
-
+import matplotlib as plt
from jass.models import plots
+from PIL import Image
+import numpy as np
from . import JassTestCase
@@ -12,10 +14,13 @@ from . import JassTestCase
class TestPlots(JassTestCase):
test_folder = "data_real"
+ expected_res_folder = "expected_graphs"
+ #expected_res_folder="baseline_images/test_plot"
def setUp(self):
# Create a temporary directory
self.test_dir = Path(tempfile.mkdtemp())
+ self.ref_res_dir=Path(os.path.join(os.path.dirname(os.path.abspath(__file__)), self.expected_res_folder))
self.worktable_hdf_path = self.get_file_path_fn("worktable-withnans.hdf5")
def tearDown(self):
@@ -24,7 +29,15 @@ class TestPlots(JassTestCase):
pass
def test_create_global_plot(self):
+ #import shutil
+ #print(plt.rcParams)
plots.create_global_plot(self.worktable_hdf_path, self.test_dir / "global_plot.png")
+ img_new=Image.open(self.test_dir /"global_plot.png")
+ img_ref=Image.open(self.ref_res_dir / "expected_global_plot.png")
+ sum_sq_diff = np.sum((np.asarray(img_new).astype('float') - np.asarray(img_ref).astype('float')) ** 2)
+ print("sum_sq_diff=",sum_sq_diff)
+ assert(sum_sq_diff==0.0)
+
def test_create_qq_plot(self):
plots.create_qq_plot(self.worktable_hdf_path, self.test_dir / "qq_plot.png")
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..e82ed6c837119abc49291a903ea65923d8a2bb31
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,46 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "jass"
+authors = [
+ {name="Hervé Ménager", email='hmenager@pasteur.fr'},
+ {name="Pierre Lechat", email='pierre.lechat@pasteur.fr'},
+ {name="Carla Lasry", email='carla.lasry@pasteur.fr'},
+ {name="Vincent Guillemot", email='vincent.guillemot@pasteur.fr'},
+ {name="Hugues Aschard", email='hugues.aschard@pasteur.fr'},
+ {name="Hanna Julienne", email='hanna.julienne@pasteur.fr'}
+]
+description="JASS allows for single SNP joint analysis of multiple GWAS summary statistics"
+readme ="README.md"
+dynamic = ["dependencies"]
+version = "2.2"
+requires-python = ">=3.6"
+
+classifiers = [
+ "Programming Language :: Python :: 3",
+ "License :: OSI Approved :: MIT License",
+ "Operating System :: OS Independent",
+]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+
+
+[tool.setuptools.packages.find]
+include = ["jass*"]
+
+[tool.setuptools.package-data]
+jass = ["swagger/swagger.yaml",
+"data/*.tsv"]
+# include-package-data = true
+
+[project.scripts]
+jass="jass.__main__:main"
+
+[project.urls]
+Homepage = "https://gitlab.pasteur.fr/statistical-genetics/jass"
+
+[project.license]
+text = "MIT"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index c705857281f43e140741316bfef400d59fa45e2c..0a12f559a15f20fde1fa2fd95e6b309d88e83728 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,4 +18,4 @@ uvicorn[standard]
typing_extensions; python_version < '3.8'
requests
h5py
-wheel
\ No newline at end of file
+wheel
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index b7e478982ccf9ab1963c74e1084dfccb6e42c583..0000000000000000000000000000000000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[aliases]
-test=pytest
diff --git a/setup.py b/setup.py
index 61bba8e85879dc9f5f6e8efca8c09667813475b9..551bbcd48835c52227ace9ca99cc62efa725dd42 100644
--- a/setup.py
+++ b/setup.py
@@ -2,56 +2,22 @@
import os
import pathlib
-import pkg_resources
-from setuptools import setup, find_packages
-NAME = "jass"
-VERSION = "2.2"
+from setuptools import setup
-SETUP_DIR = os.path.dirname(__file__)
-README = os.path.join(SETUP_DIR, 'README.md')
-readme = open(README).read()
-
-with pathlib.Path('requirements.txt').open() as requirements_txt:
- REQUIRES = [
- str(requirement)
- for requirement
- in pkg_resources.parse_requirements(requirements_txt)
- ]
-
-setup(
- name=NAME,
- version=VERSION,
- description="JASS allows for single SNP joint analysis of multiple GWAS summary statistics",
- author='Hervé Ménager and Pierre Lechat and Carla Lasry and Vincent Guillemot and Hugues Aschard and Hanna Julienne',
- author_email="hmenager@pasteur.fr, pierre.lechat@pasteur.fr, carla.lasry@pasteur.fr, vincent.guillemot@pasteur.fr, hugues.aschard@pasteur.fr, hanna.julienne@pasteur.fr",
- url="https://gitlab.pasteur.fr/statistical-genetics/jass",
- packages=find_packages(),
- install_requires=REQUIRES,
- license="MIT",
- keywords=["GWAS", "Data analysis", "summary statistics"],
- package_data={'jass': ['swagger/swagger.yaml', "data/*.tsv"]},
- include_package_data=True,
- long_description=readme,
- long_description_content_type="text/markdown",
- classifiers=[
- "Programming Language :: Python :: 3",
- "License :: OSI Approved :: MIT License",
- "Operating System :: OS Independent",
- ],
- python_requires='>=3.6',
- setup_requires=[
- 'pytest-runner',
- 'Flask-Testing'
- ],
- tests_require=[
- 'pytest',
- 'Flask-Testing'
- ],
- entry_points={
- 'console_scripts': [
- 'jass=jass.__main__:main',
- ]
- }
-)
+# NAME = "jass"
+# VERSION = "2.2"
+#
+# SETUP_DIR = os.path.dirname(__file__)
+# README = os.path.join(SETUP_DIR, 'README.md')
+# readme = open(README).read()
+#
+# with pathlib.Path('requirements.txt').open() as requirements_txt:
+# REQUIRES = [
+# str(requirement)
+# for requirement
+# in pkg_resources.parse_requirements(requirements_txt)
+# ]
+if __name__ == "__main__":
+ setup()
diff --git a/test-requirements.txt b/test-requirements.txt
deleted file mode 100644
index 7f8d96e6b40e853d658f88fa745ddcf37ff7644c..0000000000000000000000000000000000000000
--- a/test-requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-flask_testing==0.6.1
-coverage>=4.0.3
-nose>=1.3.7
-pluggy>=0.3.1
-py>=1.4.31
-randomize>=0.13