Merge remote-tracking branch 'origin/main' into sarah_matplotlib

.github/workflows/filtering-ci.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
-        python-version: ["3.11"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/ingestion-ci.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
-        python-version: ["3.11"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/integration-ci.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # , "macos-latest", "windows-latest"
-        python-version: ["3.11"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v4

CHANGELOG.md

@@ -10,7 +10,7 @@
 ### fixed
 
 - fixed error in `vis`
-    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both 
+    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
 
 ### dependencies
 

README.md

@@ -4,7 +4,7 @@
 
 ## Overview
 
-Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. 
+Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale.
 Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
 
 **See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)**  
@@ -45,4 +45,4 @@ bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https
 ## Contributors
 
 Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion.
-Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht.
+Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht, Lukas Heumos.

docs/release_notes.md

@@ -10,7 +10,7 @@
 ### fixed
 
 - fixed error in `vis`
-    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both 
+    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
 
 ### dependencies
 

panpipes/funcs/plotting.py

@@ -310,8 +310,10 @@ def ridgeplot(adata, features, layer=None, splitplot=3, bandwidth=0.1):
         ax.yaxis.set_tick_params(labelleft=True)
         ax.set_yticks(np.arange(len(features_sub)))
         ax.set_yticklabels(features_sub)
-        ax.tick_params(axis='y', which='major', labelsize=10)
-        #    tick.label.set_verticalalignment("bottom")
+        for tick in ax.get_yticklabels():
+            tick.set_fontsize(10)
+        for tick in ax.yaxis.get_major_ticks():
+            tick.label1.set_verticalalignment("bottom")
 
     fig.tight_layout()
     return fig, ax

panpipes/python_scripts/run_preprocess_prot.py

@@ -67,9 +67,6 @@
 
 
 args, opt = parser.parse_known_args()
-# args = argparse.Namespace(filtered_mudata='test.h5mu', 
-# bg_mudata='/well/cartography/users/zsj686/non_cart_projects/005-multimodal_scpipelines/ingest/test_raw.h5mu', 
-# channel_col=None, normalisation_methods='clr,dsb', clr_margin='0', quantile_clipping='True', figpath='./figures/prot', save_mtx=False, save_mudata_path='test.h5mu')
 save_mtx=pnp.pp.check_for_bool(args.save_mtx)
 
 norm_methods = args.normalisation_methods.split(',')
@@ -85,9 +82,7 @@
 sc.set_figure_params(scanpy=True, fontsize=14, dpi=300, facecolor='white', figsize=(5,5))
 
 
-
 # load filtered data - if use_muon is True this will return a mudata object, else returns an mudata object
-
 L.info("reading filtered mudata object")
 try:
     all_mdata = mu.read(args.filtered_mudata)

pyproject.toml

@@ -10,62 +10,48 @@ description = "Panpipes - multimodal single cell pipelines"
 readme = "README.md"
 
 classifiers = [
-    # Pick your license as you wish
     "License :: OSI Approved :: BSD License",
-
-    # Optional
-    # How mature is this project? Common values are
-    #   3 - Alpha
-    #   4 - Beta
-    #   5 - Production/Stable
     "Development Status :: 3 - Alpha",
-
-    # Indicate who your project is intended for
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",
     "Programming Language :: R"
     ]
 
-requires-python = ">= 3.11"
+requires-python = ">= 3.10"
 
 dependencies = [
-    "anndata>=0.8.0",
     "apsw",
     "bbknn",
     "cgatcore",
     "drmaa",
     "gevent",
     "harmonypy",
-    "jax",
-    "jaxlib",
-    "leidenalg",
-    "louvain",
-    "matplotlib",
     "mofapy2",
-    "mudata>=0.2.1",
     "muon",
-    "numpy>=1.22.4",
     "openpyxl",
-    "packaging",
-    "pandas>=1.0",
     "paramiko",
-    "pep8",
     "pysam",
-    "pynndescent",
-    "pytest",
     "pyyaml",
     "ruffus",
     "scanorama",
     "scanpy>=1.9.1",
+    "leidenalg",
+    "louvain",
     "scib",
-    "seaborn<=0.12.2",
     "scikit-misc",
     "scirpy",
     "scrublet",
     "scvi-tools>=1.1.1",
-    "sqlalchemy"]
+    "sqlalchemy",
+    ]
 
 [project.optional-dependencies]
+dev = [
+    "packaging",
+    "pytest",
+    "twine",
+    "build"
+]
 notebook = [
     "jupyter",
     "jupyterlab"
@@ -75,29 +61,13 @@ spatial = [
     "cell2location",
     "tangram-sc"
 ]
-pypi_upload = [
-    "twine",
-    "build"
-]
-
-# The following would provide a command line executable called `sample`
-# which executes the function `entry` from this package when invoked.
-[project.scripts]  # Optional
+[project.scripts]
 panpipes = "panpipes:entry.main"
 
-# This is configuration specific to the `setuptools` build backend.
-# If you are using a different build backend, you will need to change this.
 [tool.setuptools]
-# If there are data files included in your packages that need to be
-# installed, specify them here.
 package-data = {"panpipes" = ["panpipes/*/*.yml", "R_scripts/*.R", "resources/*"]}
 
 
 [build-system]
-# These are the assumed default build requirements from pip:
-# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
 requires = ["setuptools>=43.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
-
-
-#template for this file from https://github.com/pypa/sampleproject/blob/main/pyproject.toml