make alphamap optional and update installation instructions

Author: mschwoer

.github/workflows/e2e_tests_quick.yml

@@ -28,5 +28,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh tests,gui,dask
+      install-script: ./pip_install.sh tests,gui,dask,alphamap
       test-script: ./run_e2e_tests_quick.sh

.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,dask-stable,alphamap-stable
       test-script: ./run_e2e_tests_quick.sh
 
   run-unit-tests-loose:
@@ -43,5 +43,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh tests,gui,dask
+      install-script: ./pip_install.sh tests,gui,dask,alphamap
       test-script: ./run_e2e_tests_quick.sh

.github/workflows/install_and_unit_tests.yml

@@ -30,5 +30,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh tests,gui,dask
+      install-script: ./pip_install.sh tests,gui,dask,alphamap
       test-script: ./run_unit_tests.sh

.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,dask-stable,alphamap-stable
       test-script: ./run_unit_tests.sh
 
   run-unit-tests-loose:
@@ -40,5 +40,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh tests,gui,dask
+      install-script: ./pip_install.sh tests,gui,dask,alphamap
       test-script: ./run_unit_tests.sh

.github/workflows/run_example_nbs.yml

@@ -28,5 +28,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh tests,gui,dask
+      install-script: ./pip_install.sh tests,gui,dask,alphamap
       test-script: ./run_example_notebooks.sh

README.md

@@ -114,6 +114,16 @@ or the version with a pinned dependency (recommended)
 pip install "alphaquant[dask-stable]"
 ```
 
+For AlphaMap visualization features (sequence alignment plots), install the optional alphamap extra:
+
+```bash
+pip install "alphaquant[alphamap]"
+```
+or the version with a pinned dependency (recommended)
+```bash
+pip install "alphaquant[alphamap-stable]"
+```
+
 ### Developer installation
 
 AlphaQuant can also be installed in editable (i.e. developer) mode with a few `bash` commands. This allows to fully customize the software and even modify the source code to your specific needs. When an editable Python package is installed, its source code is stored in a transparent location of your choice. While optional, it is advised to first (create and) navigate to e.g. a general software folder:

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 +13,31 @@
 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 alphaquant with the 'alphamap' extra."
+    )
+    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):
-        
+
+        if not HAS_ALPHAMAP:
+            raise ImportError(
+                "alphamap is required for AlphaMapVisualizer. "
+                "Install it with: pip install \"alphaquant[alphamap]\""
+            )
+
         """
         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 
@@ -86,6 +100,11 @@ 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))

pyproject.toml

@@ -55,6 +55,8 @@ optional-dependencies = { stable = { file = ["requirements/requirements.txt",
 ] }, development = { file = ["requirements/requirements_development.txt", "requirements/requirements_tests.txt",
 ] }, dask = { file = [ "requirements/requirements_dask_loose.txt",
 ] }, dask-stable = { file = [ "requirements/requirements_dask.txt",
+] }, alphamap = { file = [ "requirements/requirements_alphamap_loose.txt",
+] }, alphamap-stable = { file = [ "requirements/requirements_alphamap.txt",
 ] }}
 
 version = {attr = "alphaquant.__version__"}