Adapt to removal of dev branch

.github/workflows/branch-checks.yaml

@@ -19,6 +19,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
+        python-version: [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}

.github/workflows/pip_installation.yml

@@ -1,14 +1,11 @@
 # Perform pip installation and run all tests
 
 # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
-# On each push to develop, the whole test matrix runs, additionally, its success is mandatory for merging to main.
+# On each push to main, the whole test matrix runs.
 # In the (assumed to be rare case) that these full matrix tests fail but the reduced matrix tests passed,
-# we will learn about it latest before pushing to main. The merge that caused the issue can then be identified
-# from the tests that ran on develop.
+# we will learn about it latest after pushing to main. The merge that caused the issue can then be identified.
 on:
   push:
-    branches: [ main, development ]
-  pull_request:
     branches: [ main ]
   workflow_dispatch:
 
@@ -20,6 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+        python-version : [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}

.readthedocs.yaml

@@ -16,9 +16,6 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF
 # formats: all
 
-# conda:
-#   environment: misc/conda_dev_env.yaml
-
 # # Optionally set the version of Python and requirements required to build your docs
 python:
   install:

MANIFEST.in

@@ -1,4 +1,9 @@
 recursive-include alphabase *
 include LICENSE.txt
 include README.md
-recursive-exclude alphabase/logs *
+
+recursive-exclude logs *
+recursive-exclude tests *
+
+global-exclude */__pycache__/*
+global-exclude *.pyc *.nbi *.nbc

README.md

@@ -101,11 +101,11 @@ NOTE: You might need to run `pip install -U pip` before installing
 AlphaBase like this. Also note the double quotes `"`.
 
 For those who are really adventurous, it is also possible to directly
-install any branch (e.g. `@development`) with any extras
+install any branch (e.g. `@main`) with any extras
 (e.g. `#egg=alphabase[stable,development]`) from GitHub with e.g.
 
 ``` bash
-pip install "git+https://github.com/MannLabs/alphabase.git@development#egg=alphabase[stable,development]"
+pip install "git+https://github.com/MannLabs/alphabase.git@main#egg=alphabase[stable,development]"
 ```
 
 ### Developer

misc/pip_install.sh

@@ -22,4 +22,4 @@ conda run -n $ENV_NAME --no-capture-output pip freeze
 
 # conda 'run' vs. 'activate', cf. https://stackoverflow.com/a/72395091
 conda run -n $ENV_NAME --no-capture-output pip install -e "../.$INSTALL_STRING"
-conda run -n $ENV_NAME --no-capture-output alphabase
+conda run -n $ENV_NAME --no-capture-output python -c "import alphabase; print('OK')" -v

pyproject.toml

@@ -48,15 +48,15 @@ find = {}
 [tool.setuptools.dynamic]
 # https://stackoverflow.com/a/73600610
 dependencies = {file = ["requirements/requirements_loose.txt"]}
-optional-dependencies = { stable = { file = ["requirements/requirements.txt",
-] }, tests = { file = [ "requirements/requirements_tests.txt",
-] }, development = { file = ["requirements/requirements_development.txt", "requirements/requirements_tests.txt", "requirements/requirements_docs.txt"
-] }}
+optional-dependencies.stable = { file = ["requirements/requirements.txt"] }
+optional-dependencies.tests = { file = [ "requirements/requirements_tests.txt"] }
+optional-dependencies.development = { file = [
+    "requirements/requirements_development.txt",
+    "requirements/requirements_tests.txt",
+    "requirements/requirements_docs.txt"
+] }
 version = {attr = "alphabase.__version__"}
 
-[project.scripts]
-alphabase = "alphabase.cli:run"
-
 
 [tool.ruff.lint]
 select =  [

ruff-lint-psm-readers.toml

@@ -13,8 +13,6 @@ exclude = [
     "test_*",
     "alphabase/__init__.py",
     "alphabase/*utils.py",
-    "alphabase/gui.py",
-    "alphabase/cli.py",
     "alphabase/quantification/*.py",
     "alphabase/smiles/*.py",
     "alphabase/protein/*.py",