Merge branch 'master' of https://github.com/sdrogers/vimms into boxco…

…ntroller

.github/workflows/python-package-conda.yml

@@ -0,0 +1,34 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

.readthedocs.yml

@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "miniconda3-4.7"
+
 # Build documentation with MkDocs
 mkdocs:
   configuration: mkdocs.yml
@@ -15,4 +20,4 @@ formats: all
 
 # Specify the Conda environment file
 conda:
-  environment: environment.yml
+  environment: environment_readthedocs.yml

Pipfile

@@ -4,44 +4,44 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-numpy = "*"
-pandas = "*"
-scipy = "*"
-matplotlib = "*"
-numba = "*"
-numba-stats = "*"
-seaborn = "*"
-plotly = "*"
-scikit-learn = "*"
-pymzml = "==2.4.7"
-psims = "*"
-events = "*"
-tqdm = "*"
-joblib = "*"
-ipyparallel = "*"
-requests = "*"
-loguru = "*"
-networkx = "*"
-jsonpickle = "*"
-statsmodels = "*"
-mass-spec-utils = "*"
-tabulate = "*"
-pysmiles = "*"
-pipenv-setup = "*"
-flake8 = "*"
-autopep8 = "*"
-pytest = "*"
-pytest-cov = "*"
-intervaltree = "*"
-jupyterlab = "*"
-ipywidgets = "*"
-gpy = "*"
+numpy = ">=1.24.3"
+pandas = ">=2.0.3"
+scipy = ">=1.11.1"
+matplotlib = ">=3.7.2"
+seaborn = ">=0.12.2"
+plotly = ">=5.9.0"
+scikit-learn = ">=1.3.0"
+tqdm = ">=4.65.0"
+joblib = ">=1.2.0"
+ipyparallel = ">=8.4.1"
+requests = ">=2.31.0"
+loguru = ">=0.5.3"
+networkx = ">=3.1"
+jsonpickle = ">=2.2.0"
+statsmodels = ">=0.14.0"
+tabulate = ">=0.8.10"
+intervaltree = ">=3.1.0"
+events = ">=0.5"
+pymzml = ">=2.4.7"
+psims = ">=1.2.7"
+mass-spec-utils = ">=0.0.12"
+pysmiles = ">=1.1.2"
+numba = ">=0.57.1"
+numba-stats = ">=1.3.0"
+ms-deisotope = ">=0.0.53"
+optuna = ">=3.3.0"
+# gpy = ">=1.10.0"
+# kaleido = ">=0.2.1"
 
 [dev-packages]
-twine = "*"
-build = "*"
-mkdocs = "*"
-mkdocstrings = "*"
+jupyterlab = ">=3.6.3"
+ipywidgets = ">=8.0.4"
+flake8 = ">=6.0.0"
+autopep8 = ">=1.6.0"
+pytest = ">=7.4.0"
+pytest-cov = ">=4.1.0"
+mkdocs = ">=1.5.3"
+mkdocstrings = ">=0.23.0"
 
 [requires]
-python_version = "3"
+python_version = "3.10"

README.md

@@ -13,6 +13,7 @@ Eager to start using ViMMS? Take advantage of these resources:
 - Visit our project documentation page: [![Documentation Status](https://readthedocs.org/projects/vimms/badge/?version=latest)](http://vimms.readthedocs.io/?badge=latest)
 - Our [Demo folder](https://github.com/glasgowcompbio/vimms/tree/master/demo) contains notebooks that demonstrate how to use the framework in a simulated environment.
 - For specific examples that accompany our publications, see the [Example folder](https://github.com/glasgowcompbio/vimms/tree/master/examples).
+- You can also find this [quick guide on how to get started using ViMMS](https://github.com/glasgowcompbio/vimms/blob/master/demo/guide_to_vimms.ipynb).
 
 # Key Features
 
@@ -22,6 +23,7 @@ Moreover, ViMMS serves as a platform for the development, optimization, and test
 
 To see a more thorough explanation of the use cases of ViMMS, please refer to the [Use Cases](pages/use_cases.md) section.
 
+
 # Contributions
 
 As an open-source project licensed under MIT, we welcomes all forms of contributions, including bug fixes, new features, and more. You can find our community contribution guidelines [here](https://github.com/glasgowcompbio/vimms/blob/master/CONTRIBUTING.md).

batch_files/FeatureFinderCentroided.ini

@@ -19,7 +19,7 @@
           <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." required="false" advanced="false" restrictions="1:" />
         </NODE>
         <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">
-          <ITEM name="mz_tolerance" value="0.03" type="double" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" required="false" advanced="false" restrictions="0.0:" />
+          <ITEM name="mz_tolerance" value="0.001" type="double" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instrument.#br#This value must be smaller than that 1/charge_high!" required="false" advanced="false" restrictions="0.0:" />
           <ITEM name="min_spectra" value="10" type="int" description="Number of spectra that have to show a similar peak mass in a mass trace." required="false" advanced="false" restrictions="1:" />
           <ITEM name="max_missing" value="1" type="int" description="Number of consecutive spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below &apos;min_spectra&apos;!" required="false" advanced="false" restrictions="0:" />
           <ITEM name="slope_bound" value="0.1" type="double" description="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to separate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." required="false" advanced="false" restrictions="0.0:" />

environment.yml

@@ -1,41 +1,44 @@
 name: vimms
 channels:
-- defaults
+  - defaults
 dependencies:
-  - python=3.9
-  - numpy
-  - pandas
-  - numba
-  - scipy
-  - matplotlib
-  - seaborn
-  - plotly
-  - scikit-learn
-  - tqdm
-  - joblib
-  - ipyparallel
-  - requests
-  - loguru
-  - networkx
-  - jsonpickle
-  - statsmodels
-  - tabulate
-  - flake8
-  - autopep8
-  - pytest
-  - pytest-cov
-  - intervaltree
-  - jupyterlab
-  - ipywidgets
+  - python>=3.9,<3.11
+  - numpy>=1.24.3
+  - pandas>=2.0.3
+  - numba>=0.57.1
+  - scipy>=1.11.1
+  - matplotlib>=3.7.2
+  - seaborn>=0.12.2
+  - plotly>=5.9.0
+  - scikit-learn>=1.3.0
+  - tqdm>=4.65.0
+  - joblib>=1.2.0
+  - ipyparallel>=8.4.1
+  - requests>=2.31.0
+  - loguru>=0.5.3
+  - networkx>=3.1
+  - jsonpickle>=2.2.0
+  - statsmodels>=0.14.0
+  - tabulate>=0.8.10
+  - flake8>=6.0.0
+  - autopep8>=1.6.0
+  - pytest>=7.4.0
+  - pytest-cov>=4.1.0
+  - intervaltree>=3.1.0
+  - jupyterlab>=3.6.3
+  - ipywidgets>=8.0.4
   - pip
   - pip:
-    - events
-    - gpy
-    - mkdocs
-    - mkdocstrings
-    - mkdocstrings[python]
-    - pymzml==2.4.7
-    - psims
-    - mass-spec-utils
-    - pysmiles
-    - numba-stats
+    - events>=0.5
+    - gpy>=1.10.0
+    - mkdocs>=1.5.3
+    - mkdocstrings>=0.23.0
+    - mkdocstrings-python>=1.7.0
+    - pymzml>=2.4.7
+    - psims>=1.2.7
+    - mass-spec-utils>=0.0.12
+    - pysmiles>=1.1.2
+    - numba-stats>=1.3.0
+    - ms-deisotope>=0.0.52
+    - optuna>=3.3.0
+    - kaleido>=0.2.1

environment_readthedocs.yml

@@ -0,0 +1,45 @@
+name: vimms
+channels:
+  - defaults
+dependencies:
+  - python>=3.9,<3.11
+  - numpy
+  - pandas
+  - numba
+  - scipy
+  - matplotlib
+  - seaborn
+  - plotly
+  - scikit-learn
+  - tqdm
+  - joblib
+  - ipyparallel
+  - requests
+  - loguru
+  - networkx
+  - jsonpickle
+  - statsmodels
+  - tabulate
+  - flake8
+  - autopep8
+  - pytest
+  - pytest-cov
+  - intervaltree
+  - jupyterlab
+  - ipywidgets
+  - pip
+  - pip:
+    - recommonmark
+    - mkdocs
+    - events
+    - gpy
+    - mkdocstrings
+    - mkdocstrings-python
+    - pymzml
+    - psims
+    - mass-spec-utils
+    - pysmiles
+    - numba-stats
+    - ms-deisotope
+    - optuna
+    - kaleido