Merge remote-tracking branch 'origin/v1_feature_branch' into refactor…

…-flashloader

.github/workflows/benchmark.yml

@@ -31,6 +31,9 @@ jobs:
           python-version: 3.9
           poetry-version: 1.8.3
 
+      - name: Install project dependencies
+        run: poetry install
+
       # Run benchmakrs
       - name: Run benchmarks on python 3.8
         run: |

.github/workflows/testing_coverage.yml

@@ -26,6 +26,9 @@ jobs:
           python-version: 3.9
           poetry-version: 1.8.3
 
+      - name: Install project dependencies
+        run: poetry install
+
       # Run pytest with coverage report, saving to xml
       - name: Run tests on python 3.9
         run: |

.github/workflows/testing_multiversion.yml

@@ -28,6 +28,9 @@ jobs:
           python-version: ${{matrix.python-version}}
           poetry-version: 1.8.3
 
+      - name: Install project dependencies
+        run: poetry install
+
       # Use cached python and dependencies, install poetry
       - name: Run tests on python ${{matrix.python-version}}
         run: |

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2023 OpenCOMPES
+Copyright (c) 2022-2024 OpenCOMPES
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/conf.py

@@ -27,7 +27,7 @@ def _get_project_meta():
 
 pkg_meta = _get_project_meta()
 project = str(pkg_meta["name"])
-copyright = "2022, OpenCOMPES team"
+copyright = "2024, OpenCOMPES team"
 author = "OpenCOMPES team"
 
 # The short X.Y version

docs/misc/contributing.rst

@@ -73,7 +73,7 @@ Development Workflow
 
 3. **Write Tests:** If your contribution introduces new features or fixes a bug, add tests to cover your changes.
 
-4. **Run Tests:** To ensure no funtionality is broken, run the tests:
+4. **Run Tests:** To ensure no functionality is broken, run the tests:
 
     .. code-block:: bash
 

docs/misc/maintain.rst

@@ -140,7 +140,7 @@ To create a release, follow these steps:
    c. **If you don't see update on PyPI:**
 
       - Visit the GitHub Actions page and monitor the Release workflow (https://github.com/OpenCOMPES/sed/actions/workflows/release.yml).
-      - Check if errors occured.
+      - Check if errors occurred.
 
 
 **Understanding the Release Workflow**

docs/sed/config.rst

@@ -1,19 +1,19 @@
 Config
 ===================================================
-The config module contains a mechanis to collect configuration parameters from various sources and configuration files, and to combine them in a hierachical manner into a single, consistent configuration dictionary.
+The config module contains a mechanics to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary.
 It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
 
 * ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.
-* ``user_config``: A config file provided by the user, stored as :file:`.sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
-* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
+* ``user_config``: A config file provided by the user, stored as :file:`.config/sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
+* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
 * ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files.
 
 The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary).
 
 
 API
 ***************************************************
-.. automodule:: sed.core.config
+.. automobile:: sed.core.config
    :members:
    :undoc-members:
 

docs/sed/dataset.rst

@@ -64,7 +64,7 @@ Setting the “use_existing” keyword to False allows to download the data in a
 Interrupting extraction has similar behavior to download and just continues from where it stopped.
 ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 
-Or if user deletes the extracted documents, it reextracts from zip file
+Or if user deletes the extracted documents, it re-extracts from zip file
 '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 
 .. code:: python

pyproject.toml

@@ -3,7 +3,7 @@ name = "sed-processor"
 packages = [
     {include = "sed"}
 ]
-version = "0.1.10a4"
+version = "0.1.10a5"
 description = "Single Event Data Frame Processor: Backend to handle photoelectron resolved datastreams"
 authors = ["OpenCOMPES team <sed-processor@mpes.science>"]
 readme = "README.md"
@@ -24,7 +24,7 @@ lmfit = ">=1.0.3"
 matplotlib = ">=3.5.1"
 natsort = ">=8.1.0"
 numba = ">=0.55.1"
-numpy = ">=1.18"
+numpy = ">=1.18, <2.0"
 pandas = ">=1.4.1"
 psutil = ">=5.9.0"
 pynxtools-mpes = ">=0.0.3"

sed/__init__.py

@@ -1,6 +1,7 @@
-"""sed module easy access APIs
+"""sed module easy access APIs."""
+import importlib.metadata
 
-"""
 from .core.processor import SedProcessor
 
+__version__ = importlib.metadata.version("sed-processor")
 __all__ = ["SedProcessor"]