merge alphamap extra with gui

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,alphamap
+      install-script: ./pip_install.sh tests,gui,dask
       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,alphamap-stable
+      install-script: ./pip_install.sh stable,tests,gui-stable,dask-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,alphamap
+      install-script: ./pip_install.sh tests,gui,dask
       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,alphamap
+      install-script: ./pip_install.sh tests,gui,dask
       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,alphamap-stable
+      install-script: ./pip_install.sh stable,tests,gui-stable,dask-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,alphamap
+      install-script: ./pip_install.sh tests,gui,dask
       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,alphamap
+      install-script: ./pip_install.sh tests,gui,dask
       test-script: ./run_example_notebooks.sh

README.md

@@ -114,16 +114,6 @@ 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:

pyproject.toml

@@ -55,8 +55,6 @@ 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__"}

requirements/requirements_alphamap.txt

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