Improve requirements

.github/workflows/nbdev_tests.yml

@@ -27,7 +27,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./loose_pip_install.sh
+          . ./pip_install.sh loose,tests
 
       - name: Unittests
         shell: bash -le {0}

.github/workflows/quick_tests.yml

@@ -32,7 +32,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./stable_pip_install.sh
+          . ./pip_install.sh stable,tests
       - name: Run pipeline
         shell: bash -le {0}
         run: |
@@ -63,7 +63,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./loose_pip_install.sh
+          . ./pip_install.sh loose,tests
       - name: Run pipeline
         shell: bash -le {0}
         run: |

.github/workflows/quick_tests_ubuntu.yml

@@ -1,6 +1,7 @@
 on:
   push:
-    branches: [ main, development ]
+  #  branches: [ main, development ]
+  # TODO: this is covered already by quick_tests.yml
   pull_request:
   workflow_dispatch:
 
@@ -27,7 +28,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./stable_pip_install.sh
+          . ./pip_install.sh stable,tests
 
       - name: Unittests
         shell: bash -le {0}

.github/workflows/ratio_tests.yml

@@ -25,7 +25,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./stable_pip_install.sh
+          . ./pip_install.sh stable,tests
 
       - name: Ratio tests
         shell: bash -le {0}

.github/workflows/unused/all_tests.yml

@@ -28,7 +28,7 @@ jobs:
         shell: bash -le {0}
         run: |
           cd misc
-          . ./loose_pip_install.sh
+          . ./pip_install.sh loose,tests
       - name: Unittests
         shell: bash -le {0}
         run: |

README.md

@@ -240,7 +240,7 @@ directLFQ is started internally via the directlfq.lfq_manager.run_lfq() command.
 -  **num_cores**: The number of cores to use (default is to use multiprocessing).
 -  **filename_suffix**: Suffix to append to the output files.
 -  **deactivate_normalization**: Set to true, if no between-sample normalization should be performed before processing.
--  **filter_dict**: In case you want to define specific filters in addition to the standard filters, you can add a yaml file where the filters are defined (see example [here](release/examples/filterdict.yaml)). In the Python API you can also directly put in the dictionary instead of the .yaml file.
+-  **filter_dict**: In case you want to define specific filters in addition to the standard filters, you can add a yaml file where the filters are defined (see example [here](misc/examples/filterdict.yaml)). In the Python API you can also directly put in the dictionary instead of the .yaml file.
 
 ---
 

misc/pip_install.sh

@@ -0,0 +1,25 @@
+#!/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:-directlfq}
+PYTHON_VERSION=${3:-3.9}
+
+conda create -n $ENV_NAME python=$PYTHON_VERSION -y
+
+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 directlfq

pyproject.toml

@@ -51,7 +51,8 @@ dependencies = {file = ["requirements/requirements_loose.txt"]}
 optional-dependencies = { stable = { file = ["requirements/requirements.txt",
 ] }, gui = { file = [ "requirements/requirements_gui_loose.txt",
 ] }, gui-stable = { file = [ "requirements/requirements_gui.txt",
-] }, development = { file = ["requirements/requirements_development.txt"
+] }, tests = { file = [ "requirements/requirements_tests.txt",
+] }, development = { file = ["requirements/requirements_development.txt", "requirements/requirements_tests.txt",
 ] }}
 
 version = {attr = "directlfq.__version__"}

release/windows/build_installer_windows.ps1

@@ -18,4 +18,3 @@ pip install "dist/$WHL_NAME[stable,gui-stable]"
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller
 pyinstaller release/pyinstaller/directlfq.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y
-# pip install jinja2==3.0

requirements/requirements.txt

@@ -1,12 +1,9 @@
 # Dependencies required for running the "stable" version of directlfq.
 # Only usage of fixed versions is allowed, and all dependencies listed here must also be
 # included in `requirements_loose.txt` (enforced by a test).
-Jinja2==3.1.2
 numpy==1.23.5
-pandas>=1.5.3  # test: tolerate_version
-dask>=2023.1.0  # test: tolerate_version
+pandas==2.2.3
+dask==2024.8.0
 numba==0.56.4
 multiprocess==0.70.14
-wget==3.2
-PyYAML==6.0.2
 pyarrow==17.0.0

requirements/requirements_development.txt

@@ -1,20 +1,9 @@
+# Dependencies helping for development
 jupyter
 jupyter_contrib_nbextensions
-pyinstaller
 autodocsumm
 sphinx-rtd-theme
-twine
 bump-my-version
 pipdeptree
 ipykernel
-tqdm
-psutil
-matplotlib_venn
-wget
-seaborn
-matplotlib
-nbdev>=2.3.9
-notebook
-alphabase>=1.4.0
-progressbar
-pytest
+notebook

requirements/requirements_loose.txt

@@ -1,11 +1,8 @@
 # Dependencies required for running the "loose" version of direclfq.
 # All dependencies that are also included in `requirements.txt` must be added also here (enforced by a test).
-Jinja2
 numpy
 pandas
 dask
 numba
 multiprocess
-wget
-PyYAML
 pyarrow

requirements/requirements_tests.txt

@@ -0,0 +1,9 @@
+# Dependencies required for running tests
+matplotlib_venn
+matplotlib
+wget
+seaborn
+nbdev>=2.3.9
+alphabase>=1.4.0
+progressbar
+pytest