Update package layout and default imports (#64)

enryH · github-actions[bot] · Copilot · web-flow · commit e0ed4d9114d4 · 2026-06-15T15:18:24.000+02:00
* 🚧 start adding core modules per default

- in the future with the default dependencies

* 📝 describe dependencies and identify core modules

- core modules dependencies should be installed always
- the other should only be installed on request

* ⚡🔧 remove some default imports

* docs: update markdown reference

* 🔧 move vuecore to documentation  deps

* 🔧 add all functionality

* docs: update markdown reference

* Improve error messages for missing modules

Co-authored-by: Copilot Autofix powered by AI &lt;175728472+Copilot@users.noreply.github.com&gt;

* 📝 update description in pyproject toml of optional dependencies

* 🔧 vuecore for current version needs all dependencies

---------

Co-authored-by: github-actions[bot] &lt;41898282+github-actions[bot]@users.noreply.github.com&gt;
Co-authored-by: Copilot Autofix powered by AI &lt;175728472+Copilot@users.noreply.github.com&gt;
diff --git a/.github/workflows/updt_markdowns.yml b/.github/workflows/updt_markdowns.yml
@@ -28,7 +28,7 @@ jobs:
       - name: Install docs dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ".[docs]" sphinx-markdown-builder==0.6.9
+          pip install ".[docs,all]" sphinx-markdown-builder==0.6.9
 
       - name: Build markdown docs
         working-directory: docs
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -32,3 +32,4 @@ python:
      path: .
      extra_requirements:
       - docs
+      - all
diff --git a/docs/api_examples/batch_correction.ipynb b/docs/api_examples/batch_correction.ipynb
@@ -27,7 +27,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore"
+    "%pip install acore vuecore"
    ]
   },
   {
diff --git a/docs/api_examples/batch_correction.py b/docs/api_examples/batch_correction.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.19.1
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -24,7 +24,7 @@
 
 
 # %% tags=["hide-output"]
-# %pip install acore
+# %pip install acore vuecore
 
 # %% tags=["hide-input"]
 from typing import Optional
diff --git a/docs/api_examples/diff_regulation_ancova.ipynb b/docs/api_examples/diff_regulation_ancova.ipynb
@@ -32,7 +32,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore"
+    "%pip install acore vuecore"
    ]
   },
   {
diff --git a/docs/api_examples/diff_regulation_ancova.py b/docs/api_examples/diff_regulation_ancova.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.19.1
+#       jupytext_version: 1.19.3
 # ---
 
 # %% [markdown]
@@ -27,7 +27,7 @@
 #
 
 # %% tags=["hide-output"]
-# %pip install acore
+# %pip install acore vuecore
 
 # %% tags=["hide-input"]
 import dsp_pandas
diff --git a/docs/api_examples/diff_regulation_anova_ttest_two_groups.ipynb b/docs/api_examples/diff_regulation_anova_ttest_two_groups.ipynb
@@ -29,7 +29,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore"
+    "%pip install acore vuecore"
    ]
   },
   {
diff --git a/docs/api_examples/diff_regulation_anova_ttest_two_groups.py b/docs/api_examples/diff_regulation_anova_ttest_two_groups.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.19.1
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: .venv
 #     language: python
@@ -29,7 +29,7 @@
 #
 
 # %% tags=["hide-output"]
-# %pip install acore
+# %pip install acore vuecore
 
 # %% tags=["hide-input"]
 import dsp_pandas
diff --git a/docs/api_examples/enrichment_analysis.ipynb b/docs/api_examples/enrichment_analysis.ipynb
@@ -32,7 +32,8 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore vuecore"
+    "# ToDo: Improve VueCore dependencies\n",
+    "%pip install acore vuecore python-louvain snfpy"
    ]
   },
   {
diff --git a/docs/api_examples/enrichment_analysis.py b/docs/api_examples/enrichment_analysis.py
@@ -14,7 +14,8 @@
 
 
 # %% tags=["hide-output"]
-# %pip install acore vuecore
+# ToDo: Improve VueCore dependencies
+# %pip install acore vuecore python-louvain snfpy
 
 # %%
 from pathlib import Path
diff --git a/docs/api_examples/imputation.ipynb b/docs/api_examples/imputation.ipynb
@@ -36,7 +36,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore"
+    "%pip install acore vuecore"
    ]
   },
   {
diff --git a/docs/api_examples/imputation.py b/docs/api_examples/imputation.py
@@ -33,7 +33,7 @@
 
 
 # %% tags=["hide-output"]
-# %pip install acore
+# %pip install acore vuecore
 
 # %% tags=["hide-input"]
 from typing import Optional
diff --git a/docs/api_examples/normalization_analysis.ipynb b/docs/api_examples/normalization_analysis.ipynb
@@ -31,7 +31,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install acore"
+    "%pip install acore vuecore"
    ]
   },
   {
diff --git a/docs/api_examples/normalization_analysis.py b/docs/api_examples/normalization_analysis.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.18.1
+#       jupytext_version: 1.19.3
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -23,7 +23,7 @@
 # Refers to the [`acore.normalization`](acore.normalization) module.
 
 # %% tags=["hide-output"]
-# %pip install acore
+# %pip install acore vuecore
 
 # %% tags=["hide-input"]
 from typing import Optional
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,26 +23,24 @@ classifiers = [
 
 dependencies = [
   "numpy",
+  # pandas stuff
   "pandas",
-  "dsp-pandas",        # has only pandas related dependencies
-  "vuecore",
+  "dsp-pandas", # https://github.com/biosustain/dsp_pandas  (import dsp_pandas)
+  # scientific computing
   "scipy",
   "scikit-learn>=1.5",
-  "networkx",
-  "biopython",
-  "combat",
+  # enrichment analysis dependencies
   "gseapy!=1.1.5",
-  "kmapper",
-  "lifelines",
-  "pingouin<0.6.0",    # ToDo: update column name changes, https://pingouin-stats.org/changelog.html#v0-6-0-february-2026
-  "python-louvain",
-  "PyWGCNA!=2.2.0",    # to fix.
-  "snfpy",
+  "pingouin<0.6.0", # ToDo: update column name changes, https://pingouin-stats.org/changelog.html#v0-6-0-february-2026
   "umap-learn",
   "statsmodels",
-  "inmoose",           # combat batch correction
+  # batch correction dependencies
+  "combat",
+  "inmoose", # combat batch correction
+  # io dependencies
   "requests",
   "rarfile",
+  # types
   "pandera",
 ]
 
@@ -56,6 +54,8 @@ docs = [
   "jupytext",
   "sphinx-copybutton",
   "sphinx-llms-txt",
+  # Multi-Omics-Analysis group package for visualisation of results in the documentation
+  "vuecore",
 ]
 dev = [
   "black[jupyter]",
@@ -70,6 +70,21 @@ dev = [
   "ipykernel",
 ]
 
+all = [ # Optional dependencies for all non-core analysis modules
+  # Publication analysis dependencies
+  "biopython",
+  # Topological Data Analysis
+  # network analysis dependencies
+  "python-louvain", # community detection for network analysis (import community)
+  "networkx",
+  # "PyWGCNA!=2.2.0", # not used?
+  # Kaplan-Meier-analysis dependencies
+  "lifelines",
+  "kmapper",
+  # network_analysis dependencies
+  "snfpy",
+]
+
 [project.urls]
 Homepage = "https://github.com/Multiomics-Analytics-Group/acore"
 Issues = "https://github.com/Multiomics-Analytics-Group/acore/issues"
diff --git a/src/acore/__init__.py b/src/acore/__init__.py
@@ -2,5 +2,32 @@
 
 import dsp_pandas  # sets up pandas formatting options
 
-__all__ = ["dsp_pandas"]
+from . import (
+    batch_correction,
+    decomposition,
+    enrichment_analysis,
+    exploratory_analysis,
+    filter_metabolomics,
+    imputation_analysis,
+    io,
+    multiple_testing,
+    normalization,
+    types,
+    utils,
+)
+
+__all__ = [
+    "dsp_pandas",
+    "decomposition",
+    "imputation_analysis",
+    "io",
+    "enrichment_analysis",
+    "filter_metabolomics",
+    "batch_correction",
+    "exploratory_analysis",
+    "multiple_testing",
+    "normalization",
+    "types",
+    "utils",
+]
 __version__ = version("acore")
diff --git a/src/acore/kaplan_meier_analysis/__init__.py b/src/acore/kaplan_meier_analysis/__init__.py
@@ -1,6 +1,14 @@
 import pandas as pd
-from lifelines import KaplanMeierFitter, NelsonAalenFitter
-from lifelines.statistics import multivariate_logrank_test
+
+try:
+    from lifelines import KaplanMeierFitter, NelsonAalenFitter
+    from lifelines.statistics import multivariate_logrank_test
+except ImportError as e:
+    raise ImportError(
+        "Error importing lifelines module. Make sure lifelines is installed. "
+        "Install it with: pip install 'acore[all]'"
+        f"\n\nError: {e}"
+    ) from e
 
 
 def get_data_ready_for_km(dfs_dict, args):
diff --git a/src/acore/network_analysis/__init__.py b/src/acore/network_analysis/__init__.py
@@ -1,7 +1,15 @@
-import community
-import networkx as nx
+try:
+    import community
+    import networkx as nx
+    import snf
+except ImportError as e:
+    raise ImportError(
+        "Error importing network analysis dependencies (community/python-louvain, networkx, snf/snfpy). "
+        "Install them with: pip install 'acore[all]'"
+        f"\n\nError: {e}"
+    ) from e
+
 import pandas as pd
-import snf
 from sklearn import cluster
 from sklearn.cluster import AffinityPropagation
 
diff --git a/src/acore/publications_analysis/__init__.py b/src/acore/publications_analysis/__init__.py
@@ -1,7 +1,16 @@
 from urllib import error
 
 import pandas as pd
-from Bio import Entrez, Medline
+
+try:
+    from Bio import Entrez, Medline
+except ImportError as e:
+    raise ImportError(
+        "Error importing Bio modules. Make sure biopython is installed. "
+        "Install it with: pip install biopython"
+        f"\n\nError: {e}"
+    ) from e
+
 
 # TODO: This should probably be changed to the email of the person installing ckg?
 Entrez.email = "kg@dtu.dk"
diff --git a/src/acore/tda_analysis/__init__.py b/src/acore/tda_analysis/__init__.py
@@ -1,4 +1,11 @@
-import kmapper as km
+try:
+    import kmapper as km
+except ImportError as e:
+    raise ImportError(
+        "Error importing kmapper module. Make sure kmapper is installed. "
+        "Install it with: pip install 'acore[all]'"
+        f"\n\nError: {e}"
+    ) from e
 import numpy as np
 from sklearn import cluster, ensemble
 
diff --git a/src/acore/wgcna_analysis.py b/src/acore/wgcna_analysis.py
@@ -0,0 +1 @@
+# TODO: only here for vuecore compatibility

-Original file line number
+Diff line change
      path: .
      extra_requirements:
       - docs
 +      - all
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@`
`27`	`27`	`},`
`28`	`28`	`"outputs": [],`
`29`	`29`	`"source": [`
`30`		`- "%pip install acore"`
	`30`	`+ "%pip install acore vuecore"`
`31`	`31`	`]`
`32`	`32`	`},`
`33`	`33`	`{`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@`
`32`	`32`	`},`
`33`	`33`	`"outputs": [],`
`34`	`34`	`"source": [`
`35`		`- "%pip install acore"`
	`35`	`+ "%pip install acore vuecore"`
`36`	`36`	`]`
`37`	`37`	`},`
`38`	`38`	`{`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@`
`29`	`29`	`},`
`30`	`30`	`"outputs": [],`
`31`	`31`	`"source": [`
`32`		`- "%pip install acore"`
	`32`	`+ "%pip install acore vuecore"`
`33`	`33`	`]`
`34`	`34`	`},`
`35`	`35`	`{`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,8 @@`
`32`	`32`	`},`
`33`	`33`	`"outputs": [],`
`34`	`34`	`"source": [`
`35`		`- "%pip install acore vuecore"`
	`35`	`+ "# ToDo: Improve VueCore dependencies\n",`
	`36`	`+ "%pip install acore vuecore python-louvain snfpy"`
`36`	`37`	`]`
`37`	`38`	`},`
`38`	`39`	`{`