Merge pull request #121 from MannLabs/make-alphamap-optional

make alphamap optional and update installation instructions

Author: mschwoer

.github/workflows/e2e_tests_quick_multiple_platforms.yml

@@ -29,7 +29,7 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh stable,tests,gui,dask-stable
+      install-script: ./pip_install.sh stable,tests,gui-stable,dask-stable
       test-script: ./run_e2e_tests_quick.sh
 
   run-unit-tests-loose:

.github/workflows/install_and_unit_tests_multiple_platforms.yml

@@ -26,7 +26,7 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh stable,tests,gui,dask-stable
+      install-script: ./pip_install.sh stable,tests,gui-stable,dask-stable
       test-script: ./run_unit_tests.sh
 
   run-unit-tests-loose:

alphaquant/plotting/alphamapviz.py

@@ -1,14 +1,10 @@
+import warnings
+
 import numpy as np
 import pandas as pd
 import anytree
 import alphaquant.utils.utils as aqutils
 import alphaquant.resources.database_loader as aq_db_loader
-
-
-import alphamap.preprocessing
-import alphamap.organisms_data
-import alphamap.sequenceplot
-import alphamap.uniprot_integration
 import alphaquant.plotting.fcviz as aq_plot_fc
 import alphaquant.plotting.colors as aq_plot_colors
 
@@ -17,13 +13,24 @@
 aqconfig.setup_logging()
 LOGGER = logging.getLogger(__name__)
 
+try:
+    import alphamap.preprocessing
+    import alphamap.organisms_data
+    import alphamap.sequenceplot
+    import alphamap.uniprot_integration
+    HAS_ALPHAMAP = True
+except ModuleNotFoundError:
+    warnings.warn(
+        "Dependency 'alphamap' not installed. If you want to use its functionality, install it with `pip install \"alphaquant[alphamap]\"` ."
+    )
+    HAS_ALPHAMAP = False
+
 
 class AlphaMapVisualizer:
     def __init__(self, condition1, condition2, results_directory, samplemap_file,
             order_along_protein_sequence = True, organism = 'Human',colorlist = aq_plot_colors.AlphaQuantColorMap().colorlist, tree_level = 'seq',
             protein_identifier = 'gene_symbol', label_rotation = 90, add_stripplot = False,
             narrowing_factor_for_fcplot = 1/14, rescale_factor_x = 1.0, rescale_factor_y = 2):
-        
         """
         Initializes an object for visualizing peptide fold changes and AlphaMap sequence alignment. 
         This class allows for the visualization of different proteins by using the visualize_protein method 
@@ -47,7 +54,12 @@ def __init__(self, condition1, condition2, results_directory, samplemap_file,
             identifier (str): Identifier for proteins. Can be 'gene_symbol' or 'uniprot_id'.
 
         """
-        
+        if not HAS_ALPHAMAP:
+            raise ImportError(
+                "alphamap is required for AlphaMapVisualizer. "
+                "Install it with: pip install \"alphaquant[alphamap]\""
+            )
+
         self._fc_visualizer = aq_plot_fc.FoldChangeVisualizer(condition1, condition2, results_directory, samplemap_file,
             order_along_protein_sequence = order_along_protein_sequence, organism = organism, colorlist = colorlist, 
             tree_level = tree_level, protein_identifier = protein_identifier, label_rotation = label_rotation, 
@@ -86,6 +98,11 @@ def visualize_protein(self, protein):
 class AlphaMapDfGenerator:
 
     def __init__(self, condpair_node, gene2protein_mapper, organism = 'Human', colorlist = []):
+        if not HAS_ALPHAMAP:
+            raise ImportError(
+                "alphamap is required for AlphaMapDfGenerator. "
+                "Install it with: pip install \"alphaquant[alphamap]\""
+            )
         self._condpair_node = condpair_node
         self._gene2protein_mapper = gene2protein_mapper
 

alphaquant/plotting/fcviz.py

@@ -3,11 +3,16 @@
 import alphaquant.cluster.cluster_utils as aqclustutils
 import alphaquant.plotting.base_functions as aq_plot_base
 import alphaquant.config.variables as aqvars
-import alphamap.organisms_data
 import alphaquant.utils.utils as aq_utils
 import alphaquant.resources.database_loader as aq_db_loader
 import re
 
+try:
+    import alphamap.organisms_data
+    HAS_ALPHAMAP = True
+except ModuleNotFoundError:
+    HAS_ALPHAMAP = False
+
 def _format_tree_label_string(labelstring: str) -> str:
     """Local copy of the tree label formatter to avoid circular imports.
 
@@ -198,6 +203,11 @@ def _load_sequences(self):
 
 
 def get_pyteomics_fasta(organism = 'Human'):
+        if not HAS_ALPHAMAP:
+            raise ImportError(
+                "alphamap is required for get_pyteomics_fasta. "
+                "Install it with: pip install \"alphaquant[alphamap]\""
+            )
         return alphamap.organisms_data.import_fasta(organism)
 
 class CondpairQuantificationInfo():

alphaquant/ui/dashboard_parts_plots_proteoforms.py

@@ -365,6 +365,12 @@ def _on_load_alphamap_clicked(self, event):
             self.visualization_elements.visible = True
             self.viz_warning_pane.object = ""  # Clear any previous warnings
 
+        except ImportError as import_error:
+            print("ImportError initializing visualizers:", str(import_error))
+            error_msg = f"AlphaMap is not installed. Install it with: pip install \"alphaquant[alphamap]\""
+            self.viz_warning_pane.object = f"### Note\n{error_msg}"
+            self.visualization_elements.visible = False
+
         except Exception as viz_error:
             print("Error initializing visualizers:", str(viz_error))
             print("Exception type:", type(viz_error))

requirements/requirements.txt

@@ -12,6 +12,5 @@ lmfit==1.3.2
 multiprocess==0.70.17
 openpyxl==3.1.5
 scikit-learn==1.6.1
-alphamap==0.2.0
 alphabase==1.6.0
 pyarrow==19.0.0

requirements/requirements_gui.txt

@@ -1,3 +1,4 @@
 plotly==5.24.1
 bokeh==3.6.2
 panel==1.6.0
+alphamap==0.2.0

requirements/requirements_gui_loose.txt

@@ -1,3 +1,4 @@
 plotly
 bokeh
 panel
+alphamap

requirements/requirements_loose.txt

@@ -13,5 +13,4 @@ multiprocess
 openpyxl
 scikit-learn
 alphabase
-alphamap
 pyarrow