Refactor code architecture

.github/workflows/build-test-codecov.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: true
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.11]
 
 
     steps:
@@ -32,8 +32,7 @@ jobs:
       run: |
         python3 -m pip install -U pip
         python3 -m pip install -U build
-        python3 -m pip install flake8 pytest
-        python3 -m pip install -r requirements.txt
+        python3 -m pip install flake8
 
     - name: Lint with flake8
       run: |
@@ -46,18 +45,16 @@ jobs:
       run: |
         python3 -m build
         # install the package in editable mode for the coverage report
-        python3 -m pip install -e .
-
-    - name: Install dependencies for coverage report
-      run: |
-        python3 -m pip install pytest pytest-cov coverage
+        python3 -m pip install -e .["pytest"]
 
     - name: Generate coverage report
       run: |
         pytest --cov --cov-report=xml --cov-report=term-missing
     - name: Upload Coverage to Codecov
       uses: codecov/codecov-action@v1
 
-    - name: raman_fitting -M make_examples
+    - name: raman_fitting run examples
+
+
       run: |
-        raman_fitting -M make_examples
+        raman_fitting run examples

.github/workflows/test-release-candidate.yaml

@@ -53,8 +53,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        # windows-latest !=> gives error in 'if' statetement
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11"]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
@@ -71,10 +70,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8
-        python -m pip install pytest pytest-cov coverage
         python -m pip install -U build
-        python -m pip install -r requirements.txt
-        python -m pip install --editable .[test]
+        python -m pip install --editable .["pytest"]
 
     - name: Sanity check with flake8
       run: |

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 # Temporary disabling hooks: SKIP=flake8 git commit -m "foo"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
         name: Check for files larger than 5 MB
@@ -13,23 +13,16 @@ repos:
         exclude: '\.Rd'
       - id: trailing-whitespace
         name: Check for trailing whitespaces (auto-fixes)
-  # - repo: https://github.com/pycqa/isort # raises an error disabled for now
-  #   rev: 5.11.2
-  #   hooks:
-  #     - id: isort
-  #       name: isort (python)
-  - repo: https://github.com/psf/black
-    rev: 23.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.2
     hooks:
-      - id: black
-        name: black - consistent Python code formatting (auto-fixes)
-        language_version: python # Should be a command that runs python3.6+
-  # - repo: https://github.com/pycqa/flake8
-  #   rev: 6.0.0
-  #   hooks:
-  #     - id: flake8
-  #       name: flake8 - Python linting
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.16.1
+    rev: v8.18.2
     hooks:
       - id: gitleaks

Dockerfile

@@ -1,11 +1,16 @@
 # set base image (host OS)
 FROM python:3.11
 
+RUN addgroup -S nonroot \
+    && adduser -S nonroot -G nonroot
+
+USER nonroot
+
 # set the working directory in the container
 WORKDIR /code
 
 # copy the dependencies file to the working directory
-COPY . .
+COPY ./raman-fitting ./raman-fitting
 
 # copy setup.cfg to work dir
 # COPY setup.cfg .
@@ -25,5 +30,4 @@ RUN pip install -e  ./
 #COPY src/ .
 
 # command to run on container start
-CMD [ "raman_fitting -M make_examples" ]
-# CMD [ "python", "./raman_fitting/docker/run_make_examples.py" ]
+CMD [ "raman_fitting run examples" ]

README.md

@@ -14,7 +14,7 @@
 
 In batch processing mode this package will index the raman data files in a chosen folder.
 First, it will try to extract a sample ID and position number from the filenames and create an index of the files in a dataframe. Over this index a preprocessing, fitting and exporting loop will start.
-There are several models, each with a different combination of typical peaks, used for fitting. Each individual typical peak is defined as a class in the deconvolution/default_peaks folder with some added literature reference in the docstring. Here, the individual peak parameter settings can also be easily adjusted for initial values, limits, shape (eg. Lorentzian, Gaussian and Voigt) or be fixed at certain initial values.
+There are several models, each with a different combination of typical peaks, used for fitting. Each individual typical peak is defined as a class in the deconvolution/default_models folder with some added literature reference in the docstring. Here, the individual peak parameter settings can also be easily adjusted for initial values, limits, shape (eg. Lorentzian, Gaussian and Voigt) or be fixed at certain initial values.
 Export is done with plots and excel files for the spectral data and fitting parameters for further analysis.
 
 
@@ -57,7 +57,7 @@ python -m pip install -e raman-fitting/
 
 In order to test the package after installation, please try the following command in a terminal CLI.
 ``` bash
-raman_fitting -M make_examples
+raman_fitting run examples
 ```
 or these commands in the Python interpreter or in a Jupyter Notebook.
 ``` python
@@ -86,7 +86,7 @@ raman_fitting
 
 # If you add a lot of files, try to check if the index is properly constructed
 # before fitting them.
-raman_fitting -M make_index
+raman_fitting make index
 
 # Location of index
 home/.raman_fitting/datafiles/results/raman_fitting_index.csv
@@ -106,7 +106,7 @@ sample2-100_3.txt => sampleID = 'sample2-100', position = 3
 ```
 ### Version
 
-The current version is v0.7.0
+The current version is v0.8.0
 
 ### Dependencies
 

pyproject.toml

@@ -10,33 +10,62 @@ authors = [
 ]
 description = "Python framework for the batch processing and deconvolution of raman spectra."
 readme = {file = "README.md", content-type = "text/markdown"}
-long_description = {file = "README.md", content-type = "text/markdown"}
 keywords = ["spectroscopy", "Raman", "fitting", "deconvolution", "batch processing", "carbonaceous materials"]
 classifiers = [
 	"License :: OSI Approved :: MIT License",
 	"Natural Language :: English",
 	"Programming Language :: Python",
 	"Programming Language :: Python :: 3 :: Only",
-	"Programming Language :: Python :: 3.7",
-	"Programming Language :: Python :: 3.8",
-	"Programming Language :: Python :: 3.9",
-	"Programming Language :: Python :: 3.10",
 	"Programming Language :: Python :: 3.11",
 	"Programming Language :: Python :: Implementation :: CPython",
 	"Programming Language :: Python :: Implementation :: PyPy",
 	"Intended Audience :: Science/Research",
 	"Topic :: Scientific/Engineering :: Physics",
 	"Topic :: Scientific/Engineering :: Chemistry",
 ]
-dynamic = ["version", "long_description"]
+dynamic = ["version"]
+dependencies = [
+	"pandas~=2.1.2",
+	"scipy~=1.11.3",
+	"lmfit~=1.2.2",
+	"matplotlib~=3.8.0",
+	"numpy~=1.26.1",
+	"tablib~=3.5.0",
+	"pydantic>=2.5",
+	"pydantic-settings>=2.1",
+	"pydantic_numpy>=4.1",
+	"loguru>=0.7",
+	"typer[all]",
+	"mpire[dill]~=2.10.0",
+]
+
+[project.optional-dependencies]
+pytest = [
+	"pytest",
+	"pytest-cov",
+	"pytest-flake8",
+	"mock",
+	"wheel"
+	]
+dev = [
+	"isort",
+	"pylint",
+	"flake8",
+	"autopep8",
+	"pydocstyle",
+	"black",
+	"bump2version",
+	"raman_fitting[pytest]"
+	]
 
 [project.urls]
 homepage = "https://pypi.org/project/raman-fitting/"
 repository = "https://github.com/MyPyDavid/raman-fitting.git"
 # documentation = "https://raman-fitting.readthedocs.io/en/latest/"
 
 [project.scripts]
-raman_fitting = "raman_fitting.interfaces:main"
+raman_fitting = "raman_fitting.interfaces.typer_cli:app"
+
 
 [tool.hatch.version]
 source = "vcs"
@@ -53,7 +82,7 @@ sources = ["src"]
 
 # testing
 [tool.pytest.ini_options]
-minversion = "6.0"
+minversion = "7.0"
 pythonpath = "src"
 addopts = [
     "--import-mode=importlib",
@@ -65,36 +94,58 @@ testpaths = [
     "tests",
 ]
 
+[tool.coverage.run]
+source = ["src"]
+omit = [
+    "*/example_fixtures/*",
+    ]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_also = [
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self\\.debug",
+
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+
+    # Don't complain if non-runnable code isn't run:
+    "if 0:",
+    "if __name__ == .__main__.:",
+
+    # Don't complain about abstract methods, they aren't run:
+    "@(abc\\.)?abstractmethod",
+    ]
+
+ignore_errors = true
+
+[tool.coverage.html]
+directory = "coverage_html_report"
+
+
 [tool.bumpversion]
-current_version = "0.7.0"
+current_version = "0.8.0"
 commit = true
 commit_args = "--no-verify"
+message = "Bump version: {current_version} → {new_version}"
 tag = true
 allow_dirty = true
 tag_name = "{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(\\.dev(?P<dev>\\d+))?"
 serialize =[
     "{major}.{minor}.{patch}.dev{dev}",
     "{major}.{minor}.{patch}"
 ]
-message = "Version updated from {current_version} to {new_version}"
 
-[[bumpversion.files]]
+[[tool.bumpversion.files]]
 filename= "README.md"
 search = "The current version is v{current_version}"
 replace = "The current version is v{new_version}"
 
-# [[bumpversion.files]]
-# filename= "src/raman_fitting/__init__.py"
-# search = "__version__ = '{current_version}'"
-# replace = "__version__ = '{new_version}'"
-
-# [[bumpversion.files]]
-# filename= "src/raman_fitting/_version.py"
-# search = "version = '{current_version}'"
-# replace = "version = '{new_version}'"
-
-[[bumpversion.files]]
+[[tool.bumpversion.files]]
 filename= "pyproject.toml"
 search = "current_version = '{current_version}'"
 replace = "current_version = '{new_version}'"