adapt to new alphabase

.github/workflows/_run_tests.yml

@@ -14,7 +14,7 @@ on:
         required: true
         type: string
 jobs:
-  pre-commit:
+  run-tests:
     runs-on: ${{ inputs.os }}
     steps:
     - uses: actions/checkout@v3
@@ -32,18 +32,16 @@ jobs:
     - name: Conda info
       shell: bash -l {0}
       run: conda info
-    - name: Perform pip installation
+    - name: Install mono
+      if: ${{ !contains(inputs.os, 'windows') }}
       shell: bash -l {0}
       run: |
-        cd misc
-        . ./${{ inputs.install-script }}
-    - name: Install additional dependencies required for testing
+        conda install mono
+    - name: Perform pip installation
       shell: bash -l {0}
       run: |
-        conda activate alpharaw
-        pip install matplotlib
-        pip install pytest nbmake==1.5.3
-        conda deactivate
+        cd misc
+        . ./${{ inputs.install-script }} alpharaw ${{ inputs.python-version }} ${{ !contains(inputs.os, 'windows') }}
     - name: Run tests
       shell: bash -l {0}
       run: |

.github/workflows/branch-checks.yaml

@@ -18,8 +18,9 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
+        python-version: [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: "loose_pip_install.sh"
+      install-script: pip_install.sh loose,tests

.github/workflows/pip_installation.yml

@@ -25,7 +25,7 @@ jobs:
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: "stable_pip_install.sh"
+      install-script: pip_install.sh stable
 
   loose_installation:
     name: Test loose pip installation on ${{ matrix.os }}
@@ -37,4 +37,4 @@ jobs:
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: "loose_pip_install.sh"
+      install-script: pip_install.sh loose

alpharaw/__init__.py

@@ -67,4 +67,5 @@ def register_all_readers():
 ]
 __extra_requirements__ = {
     "development": "extra_requirements/development.txt",
+    "tests": "extra_requirements/tests.txt",
 }

docs/tutorials/ms_methods.ipynb

@@ -23,7 +23,7 @@
     "\n",
     "from alpharaw import thermo\n",
     "import tempfile\n",
-    "from alphabase.test_data_downloader import DataShareDownloader\n",
+    "from alphabase.tools.data_downloader import DataShareDownloader\n",
     "import os\n",
     "import pandas as pd\n",
     "import numpy as np\n",

extra_requirements/development.txt

@@ -1,17 +1,9 @@
-pywin32; sys_platform=='win32'
-pythonnet; sys_platform=='win32'
-
 jupyter
-twine
 bumpversion
 pipdeptree
 ipykernel
 tqdm
 psutil
-h5py
-numba
-pandas
-numpy
 
 # sphinx
 autodocsumm
@@ -22,9 +14,4 @@ jinja2
 contextfilter
 furo
 
-alphabase>=1.1.0
-alphatims
-
-pytest
 pre-commit==3.7.0
-nbmake==1.5.3

extra_requirements/tests.txt

@@ -0,0 +1,4 @@
+matplotlib
+pytest
+nbmake==1.5.3
+requests

misc/pip_install.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+### Install the package with a given type in a defined conda environment with a define python version,
+### and call it to check if it works
+### example usage:
+### ./pip_install.sh stable my_env 3.9
+set -e -u
+
+INSTALL_TYPE=$1 # stable, loose, etc..
+ENV_NAME=${2:-alpharaw}
+PYTHON_VERSION=${3:-3.9}
+INSTALL_MONO=${4:-false}
+
+
+if [ "$INSTALL_MONO" = "true" ]; then
+  conda create -n $ENV_NAME python=$PYTHON_VERSION mono -y
+else
+  conda create -n $ENV_NAME python=$PYTHON_VERSION -y
+fi
+
+if [ "$INSTALL_TYPE" = "loose" ]; then
+  INSTALL_STRING=""
+else
+  INSTALL_STRING="[${INSTALL_TYPE}]"
+fi
+
+# print pip environment for reproducibility
+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 python -c "import alpharaw"

requirements.txt

@@ -9,6 +9,6 @@ sqlalchemy
 pyteomics
 lxml
 
-alphabase>=1.1.0
+alphabase>=1.5.0
 alphatims
 plotly