Merge branch 'main' of https://github.com/Ildar-Daminov/Python_for_li…

…terature_review_in_Scopus

.github/workflows/main.yml

@@ -0,0 +1,99 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish Docs
+
+# on: workflow_dispatch
+
+on:
+  push:
+    branches: [ main ]
+#   pull_request:
+#     branches: [ master ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "test"
+  publish:
+  # The type of runner that the job will run on
+    strategy:
+      matrix:
+#         os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest"]
+        # python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.9"]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Checkout project
+        uses: actions/checkout@v2
+
+     #----------------------------------------------
+     #-------  install & configure Python  ---------
+     #---------------------------------------------- 
+      - name: Install Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #  -----  install & configure poetry  ---------
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install main (non-optional) and dev dependencies
+        # see [tool.poetry.dependencies] and [tool.poetry.dev-dependencies]
+        # in pyproject.toml
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-root
+
+     #----------------------------------------------
+     # install your root project, if required
+     #----------------------------------------------
+      - name: Install package
+        run: |
+          poetry install
+          poetry install --extras "docs"
+          
+     #----------------------------------------------
+     # Build documentation
+     #----------------------------------------------
+      - name: Build doc
+        run: |
+          cd docs
+          poetry run make clean
+          poetry run make html
+          
+              
+      #----------------------------------------------
+      #    deploy documentation
+      #----------------------------------------------  
+      - name: Create .nojekyll file.
+        run: | 
+          > docs/_build/html/.nojekyll
+        
+      - name: Deploy documentation to gh-pages branch
+        uses: s0/git-publish-subdir-action@develop
+        env:
+          REPO: self
+          BRANCH: gh-pages
+          FOLDER: docs/_build/html
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -1,6 +1,8 @@
 
 ## Documentation
 [![Publish Docs](https://github.com/Ildar-Daminov/Python_for_literature_review_in_Scopus/actions/workflows/main.yml/badge.svg)](https://github.com/Ildar-Daminov/Python_for_literature_review_in_Scopus/actions/workflows/main.yml)
+[![Check Documentation](docs/docs_badge.svg)](https://ildar-daminov.github.io/Python_for_literature_review_in_Scopus/)
+
 
 ![Python_for_literature_review](https://user-images.githubusercontent.com/73365375/208320965-24fe4441-5ca9-4749-bb73-f17045f511e1.jpg)
 
@@ -21,9 +23,9 @@ Output:
 <p align="center">Figure 1 - Input and outputs of Python module </p>
 
 
-## Increased view of a population graph: 
+## Zoom of a population graph: 
 Interactive graph (shown above and its increased view below) representing the population of papers on a given topic consists of blue dots and lines.
-Each blue dot represents an article and lines between these dots represents their "connection". Here, a connection appears if one of the paper cites another one. 
+Each blue dot represents an article and lines between these dots represent their "connection". Here, a connection appears if one of the paper cites another one. 
 ![increased_view](https://user-images.githubusercontent.com/73365375/208321127-40c12253-d77d-4fd7-af8c-2f91d962877d.jpg)
 <p align="center">Figure 2 - Interactive graph as the output of Python code and its increased view. Blue dots are articles on a given topic and lines are their connections </p>
 
@@ -32,8 +34,11 @@ After processing your query, Python generates a excel file with papers correspon
 ![list](https://user-images.githubusercontent.com/73365375/210182373-5b234e04-1020-4d17-8c8f-2c8be3f59a2c.jpg)
 <p align="center">Figure 3 - The example of excel file with the papers on the topic of hosting capacity </p>
 
-Note: In additon to this excel file, Python generates npy files with the list of publications outside Scopus and papers with the error like 404 (such situation happens if paper in Scopus is not correctly filled e.g. empty title, authors names, abstract etc). These npy files can be further processed to doublecheck of relevant papers ( not included in current version of module yet)
+Note: In additon to this excel file, Python generates npy files with the list of publications outside Scopus and papers with the error like 404 (such situation happens if paper in Scopus is not correctly filled e.g. empty title, authors names, abstract etc). These npy files can be further processed to doublecheck of relevant papers (this doublechecking is not included in current version of module yet)
 
+## Python workflow: how does it work
+![Python_workflow](https://user-images.githubusercontent.com/73365375/212465231-c2ff4e45-8f3d-4970-9d92-caaf4c928145.png)
+<p align="center">Figure 4 - Workflow of how a paper population is reconstructed inside of the python tool </p>
 
 # Before getting started:
 First of all, you need to ensure an access to Scopus API via pybliometrics:
@@ -61,3 +66,11 @@ Using a poetry to install all neccesary packages and run a code
 8. Run ```main_test.py``` 
 9. After the message <<<< Analysis is finished >>>>, check the resuts in the excel file <name>_outputs.xlsx and/or interactive graph
 
+# Quick start:
+Once you installed everything, you can simply change the input data (see Figure 5) and run your case studies. You may find the eid of your reference paper on its Scopus webpage (see example on Figure 6). 
+![Python code](https://user-images.githubusercontent.com/73365375/211420715-443bd84d-c3ea-468c-965f-fb653241b07f.png)
+<p align="center">Figure 5 - The only input data to be changed in order to run your case in main_test.py </p>
+
+  ![Scopus eid](https://user-images.githubusercontent.com/73365375/212465607-e63baf1f-f51c-4d15-84e7-9dbfbce24346.png)
+Figure 6 - The way how you may find the Scopus eid e.g. [2-s2.0-85101235827](https://www.scopus.com/record/display.uri?eid=2-s2.0-85101235827&origin=resultslist&sort=plf-f&src=s&sid=f716326e8305eae7e14603a5323abd22&sot=b&sdt=b&s=TITLE-ABS-KEY%28assessment+AND+dynamic+AND+transformer+AND+rating%29&sl=52&sessionSearchId=f716326e8305eae7e14603a5323abd22#abstract). 
+