pcdl release v4.1.8

.github/workflows/apple.yml

@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.14"]
-        python-version: ["3.11", "3.12", "3.13"]
+        #python-version: ["3.15"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     env:
       MPLBACKEND: Agg  # https://github.com/orgs/community/discussions/26434
@@ -34,7 +34,7 @@ jobs:
       run: |
         brew install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy vtk "ome-zarr<0.14.0"
+        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff geopandas matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy shapely spatialdata vtk
         python -m pip install /Users/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8

.github/workflows/linux.yml

@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.14"]
-        python-version: ["3.11", "3.12", "3.13"]
+        #python-version: ["3.15"]
+        python-version: ["3.12", "3.13","3.14"]
 
     env:
       MPLBACKEND: Agg  # https://github.com/orgs/community/discussions/26434
@@ -35,7 +35,7 @@ jobs:
         sudo apt update
         sudo apt install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy vtk "ome-zarr<0.14.0"
+        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff geopandas matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy shapely spatialdata vtk
         python -m pip install /home/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8

.github/workflows/windows.yml

@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.14"]
-        python-version: ["3.11", "3.12", "3.13"]
+        #python-version: ["3.15"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     env:
       MPLBACKEND: Agg  # https://github.com/orgs/community/discussions/26434
@@ -34,7 +34,7 @@ jobs:
       run: |
         choco install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy vtk "ome-zarr<0.14.0"
+        python -m pip install flake8 pytest anndata bioio bioio-ome-tiff geopandas matplotlib networkx neuroglancer numpy pandas requests scikit-image scipy shapely spatialdata vtk
         python -m pip install D:\a\physicelldataloader\physicelldataloader -v
         #echo 'set PYTHONPATH=D:\a\physicelldataloader\physicelldataloader' >> $GITHUB_ENV
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

.gitignore

@@ -18,3 +18,6 @@ pcdl.egg-info/
 
 # jupyter
 **/.ipynb_checkpoints/
+
+# galaxy
+tool_test_output*

README.md

@@ -131,6 +131,12 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
 
 ## Release Notes:
 
++ version 4.1.8 (2026-08-26): elmbeech/physicelldataloader
+    + branch v4 compatible with bioconda and galaxy.
+
++ version 4.1.7 (2026-08-21): elmbeech/physicelldataloader
+    + compatible with pandas v3.0.0.
+
 + version 4.1.6 (2026-08-20): elmbeech/physicelldataloader
     + pcdl installs now by default lightweight with only the core dependencies; users are prompted to install optional libraries if necessary. special thanks to Heber Rocha!
 

jakku/biocondarecipes_recipes/pcdl/meta.yaml

@@ -0,0 +1,91 @@
+{% set name = "pcdl" %}
+{% set version = "4.1.8" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pcdl-{{ version }}.tar.gz
+  sha256: e1bc3f1c6a645037eb5dead5aa013e9d62cd51a069daf85090976f52ddf4d829
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - pcdl_get_version = pcdl.commandline:get_version
+    - pcdl_get_unit_dict = pcdl.commandline:get_unit_dict
+    - pcdl_get_substrate_list = pcdl.commandline:get_substrate_list
+    - pcdl_get_conc_attribute = pcdl.commandline:get_conc_attribute
+    - pcdl_get_conc_df = pcdl.commandline:get_conc_df
+    - pcdl_plot_contour = pcdl.commandline:plot_contour
+    - pcdl_make_conc_vtk = pcdl.commandline:make_conc_vtk
+    - pcdl_get_celltype_list = pcdl.commandline:get_celltype_list
+    - pcdl_get_cell_attribute_list = pcdl.commandline:get_cell_attribute_list
+    - pcdl_get_cell_attribute = pcdl.commandline:get_cell_attribute
+    - pcdl_get_cell_df = pcdl.commandline:get_cell_df
+    - pcdl_get_anndata = pcdl.commandline:get_anndata
+    - pcdl_make_graph_gml = pcdl.commandline:make_graph_gml
+    - pcdl_plot_scatter = pcdl.commandline:plot_scatter
+    - pcdl_make_cell_vtk = pcdl.commandline:make_cell_vtk
+    - pcdl_plot_timeseries = pcdl.commandline:plot_timeseries
+    - pcdl_make_gif = pcdl.commandline:make_gif
+    - pcdl_make_movie = pcdl.commandline:make_movie
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.11,<4.0
+    - hatchling
+    - pip
+  run:
+    - python >=3.11,<4.0
+    - matplotlib-base
+    - numpy
+    - pandas >=2.2.2
+    - scipy >=1.13.0
+    - anndata >=0.10.8
+    - requests
+    - vtk
+    - imagemagick
+    - ffmpeg
+
+test:
+  imports:
+    - pcdl
+  commands:
+    - pcdl_get_version --help
+    - pcdl_get_unit_dict --help
+    - pcdl_get_substrate_list --help
+    - pcdl_get_conc_attribute --help
+    - pcdl_get_conc_df --help
+    - pcdl_plot_contour --help
+    - pcdl_make_conc_vtk --help
+    - pcdl_get_celltype_list --help
+    - pcdl_get_cell_attribute_list --help
+    - pcdl_get_cell_attribute --help
+    - pcdl_get_cell_df --help
+    - pcdl_get_anndata --help
+    - pcdl_make_graph_gml --help
+    - pcdl_plot_scatter --help
+    - pcdl_make_cell_vtk --help
+    - pcdl_plot_timeseries --help
+    - pcdl_make_gif --help
+    - pcdl_make_movie --help
+
+about:
+  summary: "physicell data loader (pcdl) provides a platform independent, python3 based, pip installable interface to transform output, generated with the PhysiCell agent based modeling framework, into standard formats."
+  home: "https://github.com/elmbeech/physicelldataloader"
+  dev_url: "https://github.com/elmbeech/physicelldataloader"
+  license: "BSD-3-Clause"
+  license_family: BSD
+  license_file: LICENSE
+  doc_url: "https://github.com/elmbeech/physicelldataloader/blob/v{{ version }}/README.md"
+
+extra:
+  recipe-maintainers:
+    - elmbeech
+  autobump:
+    enable: False  # see https://github.com/bioconda/bioconda-recipes/pull/57971

jakku/toolsiuc_tools/pcdl/.shed.yml

@@ -0,0 +1,17 @@
+name: pcdl
+owner: iuc
+description: pcdl PhysiCell Data Loader.
+long_description: Galaxy wrapper for the pcdl PhysiCell Data Loader command line commands for downstream analysis from PhysiCell output.
+homepage_url: https://github.com/elmbeech/physicelldataloader
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl
+type: unrestricted
+categories: [Systems Biology, Data Export, Graphics]
+
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Galaxy wrapper for physicell dataloader function: {{ tool_name }}."
+
+suite:
+  name: suite_pcdl
+  description: Galaxy wrapper suite for the pcdl PhysiCell Data Loader command line commands.
+  long_description: Galaxy wrapper suite for the pcdl PhysiCell Data Loader command line commands. Pcdl is paramount for downstream analysis from PhysiCell output. As such, the pcdl Galaxy tools are useful if you work with the interactive PhysiCell Studio Galaxy tool.

jakku/toolsiuc_tools/pcdl/README.txt

@@ -0,0 +1,23 @@
+pcdl
+====
+
+Galaxy wrapper for the pcdl PhysiCell Data Loader command line commands.
+Pcdl is paramount for downstream analysis from PhysiCell output.
+As such, the pcdl Galaxy tools are useful if you work with the interactive
+PhysiCell Studio Galaxy tool.
++ https://usegalaxy.eu/?tool_id=interactive_tool_pcstudio&version=latest
+
+You will have to unzip the PhysiCell output folder before you can run
+pcdl Galaxy tools on it.
++ https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Funzip%2Funzip%2F6.0%2Bgalaxy0&version=latest
++ https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frheiland%2Fphysicell_studio%2Finteractive_tool_pcstudio%2F0.3&version=latest
+
+More information about PhysiCell, PhysiCell Studio, and PhysiCell Data Loader
+can be found here:
++ https://physicell.org/index.html
++ https://physicell-studio.readthedocs.io/en/latest/index.html
++ https://github.com/elmbeech/physicelldataloader
+
+Date: 2025-06-06
+License: BSD-3-Clause
+Author: Elmar Bucher

jakku/toolsiuc_tools/pcdl/pcdl_get_anndata.xml

@@ -0,0 +1,128 @@
+<tool id="pcdl_get_anndata" name="pcdl_get_anndata" version="3.0.1+galaxy0" profile="21.05">
+    <macros>
+        <import>pcdl_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirement"/>
+    </requirements>
+    <command><![CDATA[
+        #import re
+        mkdir output_pc &&
+        #for $file in $path:
+            #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
+            ln -s '$file' output_pc/$filename &&
+        #end for
+
+        pcdl_get_anndata 'output_pc' $entropy
+        --custom_data_type $custom_data_type
+        --microenv $microenv
+        --graph $graph
+        --physiboss $physiboss
+        --settingxml 'none'
+        --verbose $verbose
+        --drop $drop
+        --keep $keep
+        --scale maxabs
+        --collapse $collapse
+    ]]></command>
+    <inputs>
+        <section name="essential" title="essential:" expanded="true">
+            <expand macro="path"/>
+            <expand macro="entropy"/>
+            <expand macro="custom_data_type"/>
+            <expand macro="drop"/>
+            <expand macro="keep"/>
+            <expand macro="scale"/>
+            <expand macro="collapse"/>
+        </section>
+        <section name="advanced" title="advanced:" expanded="false">
+            <expand macro="microenv"/>
+            <expand macro="graph"/>
+            <expand macro="physiboss"/>
+            <expand macro="verbose"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="anndata_h5ad" type="list">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.h5ad" format="h5ad" directory="output_pc" visible="false"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <section name="essential">
+                <param name="path">
+                    <expand macro="output"/>
+                </param>
+                <param name="collapse" value="true"/>
+            </section>
+            <section name="advanced">
+                <param name="verbose" value="true"/>
+            </section>
+            <output_collection name="anndata_h5ad" count="1">
+                <element name="timeseries_cell_maxabs">
+                    <assert_contents>
+                        <has_h5_keys keys="X"/>
+                        <has_h5_keys keys="layers"/>
+                        <has_h5_keys keys="obs/z_layer, obs/time, obs/ID, obs/cell_type, obs/chemotaxis_index, obs/current_death_model, obs/current_phase, obs/cycle_model"/>
+                        <has_h5_keys keys="obsm/spatial"/>
+                        <has_h5_keys keys="uns"/>
+                        <has_h5_keys keys="var/_index"/>
+                        <has_h5_keys keys="varm"/>
+                        <has_h5_keys keys="varp"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <section name="essential">
+                <param name="path">
+                    <expand macro="output"/>
+                </param>
+                <param name="collapse" value="false"/>
+            </section>
+            <section name="advanced">
+                <param name="verbose" value="false"/>
+            </section>
+            <output_collection name="anndata_h5ad" count="2">
+                <element name="output00000000_cell_maxabs">
+                    <assert_contents>
+                        <has_h5_keys keys="X"/>
+                        <has_h5_keys keys="layers"/>
+                        <has_h5_keys keys="obs/z_layer, obs/time, obs/ID, obs/cell_type, obs/chemotaxis_index, obs/current_death_model, obs/current_phase, obs/cycle_model"/>
+                        <has_h5_keys keys="obsm/spatial"/>
+                        <has_h5_keys keys="uns"/>
+                        <has_h5_keys keys="var/_index"/>
+                        <has_h5_keys keys="varm"/>
+                        <has_h5_keys keys="varp"/>
+                    </assert_contents>
+                </element>
+                <element name="output00000001_cell_maxabs">
+                    <assert_contents>
+                        <has_h5_keys keys="X"/>
+                        <has_h5_keys keys="layers"/>
+                        <has_h5_keys keys="obs/z_layer, obs/time, obs/ID, obs/cell_type, obs/chemotaxis_index, obs/current_death_model, obs/current_phase, obs/cycle_model"/>
+                        <has_h5_keys keys="obsm/spatial"/>
+                        <has_h5_keys keys="uns"/>
+                        <has_h5_keys keys="var/_index"/>
+                        <has_h5_keys keys="varm"/>
+                        <has_h5_keys keys="varp"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Function to transform mcds time steps into one or many anndata objects for downstream analysis.
+
+Scale parameter details: Possible values are None, maxabs, minmax, std.
+None: no scaling. Set scale to None if you would like to have raw data or entirely scale, transform, and normalize the data later. 
+Maxabs: maximum absolute value distance scaler will linearly map all values into a [-1, 1] interval. If the original data has no negative values, the result will be the same as with the minmax scaler (except with attributes with only one value). If the attribute has only zeros, the value will be set to 0. 
+Minmax: minimum maximum distance scaler will map all values linearly into a [0, 1] interval. If the attribute has only one value, the value will be set to 0.
+Std: standard deviation scaler will result in sigmas. Each attribute will be mean centered around 0. Ddof delta degree of freedom is set to 1 because it is assumed that the values are samples out of the population and not the entire population. It is incomprehensible to me that the equivalent sklearn method has ddof set to 0. If the attribute has only one value, the value will be set to 0.
+
+Homepage: https://github.com/elmbeech/physicelldataloader
+    ]]></help>
+    <citations>
+        <expand macro="citation"/>
+    </citations>
+</tool>