Merge pull request #20 from KShebek/master

Merging KShebek fork into tyo-nu.
tyo-nu · Mar 23, 2021 · 1253d87 · 1253d87
2 parents fd01a0b + 49bc653
commit 1253d87
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diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -0,0 +1,35 @@
+name: MINE-Database
+
+on: [push, pull_request]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Add conda to system path
+      run: |
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies and create base conda environment
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 tox black flake8-bugbear flake8-docstrings isort tox
+        conda env update --file environment.yml --name base
+        conda install pytest pytest-cov
+        conda develop ../MINE-Database
+    - name: Run tox to determine formatting and safety
+      if: always()
+      run: |
+        tox
+    - name: Test with pytest
+      if: always()
+      run: |
+        pytest
diff --git a/.gitignore b/.gitignore
@@ -79,10 +79,13 @@ Scripts/cfm_id/esi_msms_models/*
 # Models
 Models/
 
-# mongod credentials
-credentials.csv
+# mongod uri
+mongo_uri.csv
 
 # misc
 local_data/
 .vscode/
-.DS_Store
+.DS_Store
+
+# MS2
+msrb-fragmenter/
diff --git a/.swp b/.swp
diff --git a/Docs/.buildinfo b/Docs/.buildinfo
diff --git a/Docs/.doctrees/environment.pickle b/Docs/.doctrees/environment.pickle
diff --git a/Docs/.doctrees/index.doctree b/Docs/.doctrees/index.doctree
diff --git a/Docs/.doctrees/minedatabase.doctree b/Docs/.doctrees/minedatabase.doctree
diff --git a/Docs/.doctrees/modules.doctree b/Docs/.doctrees/modules.doctree
diff --git a/Docs/.doctrees/pickaxe.doctree b/Docs/.doctrees/pickaxe.doctree
diff --git a/Docs/_modules/index.html b/Docs/_modules/index.html
diff --git a/Docs/_modules/minedatabase/compound_io.html b/Docs/_modules/minedatabase/compound_io.html
diff --git a/Docs/_modules/minedatabase/databases.html b/Docs/_modules/minedatabase/databases.html
diff --git a/Docs/_modules/minedatabase/pickaxe.html b/Docs/_modules/minedatabase/pickaxe.html
diff --git a/Docs/_modules/minedatabase/queries.html b/Docs/_modules/minedatabase/queries.html
diff --git a/Docs/_modules/minedatabase/utils.html b/Docs/_modules/minedatabase/utils.html
diff --git a/Docs/_sources/index.rst.txt b/Docs/_sources/index.rst.txt
diff --git a/Docs/_sources/minedatabase.rst.txt b/Docs/_sources/minedatabase.rst.txt
diff --git a/Docs/_sources/modules.rst.txt b/Docs/_sources/modules.rst.txt
diff --git a/Docs/_sources/pickaxe.rst.txt b/Docs/_sources/pickaxe.rst.txt
diff --git a/Docs/_static/ajax-loader.gif b/Docs/_static/ajax-loader.gif