From 578891deda589eafebe31126dab80a0302740801 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 22 Jan 2025 11:50:06 +0100
Subject: [PATCH 1/5] adapt to new alphabase

---
 docs/tutorials/ms_methods.ipynb | 2 +-
 requirements.txt                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/tutorials/ms_methods.ipynb b/docs/tutorials/ms_methods.ipynb
index 10065a4..346cfd0 100644
--- a/docs/tutorials/ms_methods.ipynb
+++ b/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",
diff --git a/requirements.txt b/requirements.txt
index 688d120..090c50b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,6 +9,6 @@ sqlalchemy
 pyteomics
 lxml
 
-alphabase>=1.1.0
+alphabase>=1.5.0
 alphatims
 plotly

From 74dfc58cd6bbc2a66753c7d6f02ca91fad163ed6 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 22 Jan 2025 11:59:18 +0100
Subject: [PATCH 2/5] fix tests

---
 .github/workflows/_run_tests.yml       |  9 ++++++--
 .github/workflows/branch-checks.yaml   |  2 +-
 .github/workflows/pip_installation.yml |  4 ++--
 misc/loose_pip_install.sh              |  5 -----
 misc/pip_install.sh                    | 31 ++++++++++++++++++++++++++
 misc/stable_pip_install.sh             |  5 -----
 tests/run_tests.sh                     |  0
 7 files changed, 41 insertions(+), 15 deletions(-)
 delete mode 100644 misc/loose_pip_install.sh
 create mode 100644 misc/pip_install.sh
 delete mode 100644 misc/stable_pip_install.sh
 mode change 100644 => 100755 tests/run_tests.sh

diff --git a/.github/workflows/_run_tests.yml b/.github/workflows/_run_tests.yml
index 199c09f..2121913 100644
--- a/.github/workflows/_run_tests.yml
+++ b/.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
@@ -32,11 +32,16 @@ jobs:
     - name: Conda info
       shell: bash -l {0}
       run: conda info
+    - name: Install mono
+      if: ${{ !contains(inputs.os, 'windows') }}
+      shell: bash -l {0}
+      run: |
+        conda install mono
     - name: Perform pip installation
       shell: bash -l {0}
       run: |
         cd misc
-        . ./${{ inputs.install-script }}
+        . ./${{ inputs.install-script }} alpharaw ${{ inputs.python-version }} ${{ !contains(inputs.os, 'windows') }}
     - name: Install additional dependencies required for testing
       shell: bash -l {0}
       run: |
diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
index 0d1c2bb..50a38c6 100644
--- a/.github/workflows/branch-checks.yaml
+++ b/.github/workflows/branch-checks.yaml
@@ -22,4 +22,4 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: "loose_pip_install.sh"
+      install-script: pip_install.sh loose
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index 0edff52..5eba6b0 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.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
diff --git a/misc/loose_pip_install.sh b/misc/loose_pip_install.sh
deleted file mode 100644
index e230aba..0000000
--- a/misc/loose_pip_install.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-conda create -n alpharaw python=3.9 -y
-conda activate alpharaw
-pip install -e '../.[development]'
-python -c "import alpharaw"
-conda deactivate
diff --git a/misc/pip_install.sh b/misc/pip_install.sh
new file mode 100644
index 0000000..bc25a46
--- /dev/null
+++ b/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"
diff --git a/misc/stable_pip_install.sh b/misc/stable_pip_install.sh
deleted file mode 100644
index c206240..0000000
--- a/misc/stable_pip_install.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-conda create -n alpharaw python=3.9 -y
-conda activate alpharaw
-pip install -e '../.[stable,development-stable]'
-python -c "import alpharaw"
-conda deactivate
diff --git a/tests/run_tests.sh b/tests/run_tests.sh
old mode 100644
new mode 100755

From a272e7e9ed90a8018e11e47a49442d4c6fa5e1db Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 22 Jan 2025 12:02:54 +0100
Subject: [PATCH 3/5] fix tests

---
 .github/workflows/branch-checks.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
index 50a38c6..1f985fa 100644
--- a/.github/workflows/branch-checks.yaml
+++ b/.github/workflows/branch-checks.yaml
@@ -18,6 +18,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
+        python-version: [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}

From 1ddb2754d8b2890c3cdb7f7b3ae232535ed269fe Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 22 Jan 2025 12:52:27 +0100
Subject: [PATCH 4/5] fix tests

---
 .github/workflows/_run_tests.yml     |  7 -------
 .github/workflows/branch-checks.yaml |  2 +-
 alpharaw/__init__.py                 |  1 +
 extra_requirements/development.txt   | 13 -------------
 extra_requirements/tests.txt         |  4 ++++
 5 files changed, 6 insertions(+), 21 deletions(-)
 create mode 100644 extra_requirements/tests.txt

diff --git a/.github/workflows/_run_tests.yml b/.github/workflows/_run_tests.yml
index 2121913..1271ed4 100644
--- a/.github/workflows/_run_tests.yml
+++ b/.github/workflows/_run_tests.yml
@@ -42,13 +42,6 @@ jobs:
       run: |
         cd misc
         . ./${{ inputs.install-script }} alpharaw ${{ inputs.python-version }} ${{ !contains(inputs.os, 'windows') }}
-    - name: Install additional dependencies required for testing
-      shell: bash -l {0}
-      run: |
-        conda activate alpharaw
-        pip install matplotlib
-        pip install pytest nbmake==1.5.3
-        conda deactivate
     - name: Run tests
       shell: bash -l {0}
       run: |
diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
index 1f985fa..3029e44 100644
--- a/.github/workflows/branch-checks.yaml
+++ b/.github/workflows/branch-checks.yaml
@@ -23,4 +23,4 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: pip_install.sh loose
+      install-script: pip_install.sh loose,tests
diff --git a/alpharaw/__init__.py b/alpharaw/__init__.py
index 03caef5..6505175 100644
--- a/alpharaw/__init__.py
+++ b/alpharaw/__init__.py
@@ -67,4 +67,5 @@ def register_all_readers():
 ]
 __extra_requirements__ = {
     "development": "extra_requirements/development.txt",
+    "tests": "extra_requirements/tests.txt",
 }
diff --git a/extra_requirements/development.txt b/extra_requirements/development.txt
index 6b8c7e8..534f813 100644
--- a/extra_requirements/development.txt
+++ b/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
diff --git a/extra_requirements/tests.txt b/extra_requirements/tests.txt
new file mode 100644
index 0000000..ccd0b8a
--- /dev/null
+++ b/extra_requirements/tests.txt
@@ -0,0 +1,4 @@
+matplotlib
+pytest
+nbmake==1.5.3
+requests

From 9ccd991883aeac37cd506b2a6a676876d73411ad Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 22 Jan 2025 13:07:31 +0100
Subject: [PATCH 5/5] fix tests

---
 extra_requirements/tests.txt | 1 +
 tests/run_tests.sh           | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/extra_requirements/tests.txt b/extra_requirements/tests.txt
index ccd0b8a..132a2f0 100644
--- a/extra_requirements/tests.txt
+++ b/extra_requirements/tests.txt
@@ -1,4 +1,5 @@
 matplotlib
+seaborn
 pytest
 nbmake==1.5.3
 requests
diff --git a/tests/run_tests.sh b/tests/run_tests.sh
index c383dfc..a00bcb5 100755
--- a/tests/run_tests.sh
+++ b/tests/run_tests.sh
@@ -3,4 +3,4 @@ TUTORIAL_NBS=$(find ../docs/tutorials -name "*.ipynb")
 
 ALL_NBS=$(echo $TEST_NBS$'\n'$TUTORIAL_NBS)
 
-python -m pytest --nbmake $(echo $ALL_NBS)
+python -m pytest --nbmake $(echo $ALL_NBS)  --nbmake-timeout=1800