From b6bab806480d19884c13ef5cd4b0a4ef7cc093a9 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 2 Jan 2023 14:30:52 +0100 Subject: [PATCH 01/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bf1f633..10e73bb 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Output: ## Increased view 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)

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

From 3bfb859887bd0a6e21d2c8fb9f6e1b41917d2eaa Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 2 Jan 2023 14:32:15 +0100 Subject: [PATCH 02/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 10e73bb..4b80160 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ 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)

Figure 3 - The example of excel file with the papers on the topic of hosting capacity

-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) # Before getting started: From 5e56a4ba4cbafcb32af3b2bc9df76c770bf81500 Mon Sep 17 00:00:00 2001 From: "J.M" <62579770+jmiramont@users.noreply.github.com> Date: Mon, 9 Jan 2023 16:45:56 +0100 Subject: [PATCH 03/18] add workflow file --- .github/workflows/main.yml | 53 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 .github/workflows/main.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 0000000..73f5683 --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,53 @@ +# 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 }} + + #---------------------------------------------- + # deploy documentation + #---------------------------------------------- + - name: Create .nojekyll file. + run: | + > .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 }} From 20f2406ad61edf269de243df21d9b757e75e0952 Mon Sep 17 00:00:00 2001 From: "J.M" <62579770+jmiramont@users.noreply.github.com> Date: Mon, 9 Jan 2023 16:56:58 +0100 Subject: [PATCH 04/18] Add files via upload --- docs/docs_badge.svg | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 docs/docs_badge.svg diff --git a/docs/docs_badge.svg b/docs/docs_badge.svg new file mode 100644 index 0000000..ef0ca8f --- /dev/null +++ b/docs/docs_badge.svg @@ -0,0 +1,20 @@ + + docs: latest + + + + + + + + + + + + + \ No newline at end of file From 2f21545a5cce930de98e7a8c4ca6d39c57536166 Mon Sep 17 00:00:00 2001 From: jmiramont Date: Mon, 9 Jan 2023 17:01:57 +0100 Subject: [PATCH 05/18] Adding docs badge --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 4b80160..aab3f09 100644 --- a/README.md +++ b/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) From 98d3be4d704ca6c49b5f064254e58b7214169add Mon Sep 17 00:00:00 2001 From: "J.M" <62579770+jmiramont@users.noreply.github.com> Date: Mon, 9 Jan 2023 17:16:18 +0100 Subject: [PATCH 06/18] Update main.yml --- .github/workflows/main.yml | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 73f5683..6c38b54 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -36,6 +36,52 @@ jobs: 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 From a25dfa8c76a38d84a4954f041c51ca4213ef6b0b Mon Sep 17 00:00:00 2001 From: "J.M" <62579770+jmiramont@users.noreply.github.com> Date: Mon, 9 Jan 2023 17:22:44 +0100 Subject: [PATCH 07/18] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6c38b54..05810cb 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -88,7 +88,7 @@ jobs: #---------------------------------------------- - name: Create .nojekyll file. run: | - > .nojekyll + > docs/_build/html/.nojekyll - name: Deploy documentation to gh-pages branch uses: s0/git-publish-subdir-action@develop From 00bc8ba03d14e77d644c625b0d8ebf7000333ce0 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 9 Jan 2023 22:42:25 +0100 Subject: [PATCH 08/18] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index aab3f09..8698af3 100644 --- a/README.md +++ b/README.md @@ -36,6 +36,9 @@ After processing your query, Python generates a excel file with papers correspon 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/73365375/211413581-1a489dd0-7a07-4950-8a28-06523674b201.png) +

Figure 4 - How python tool analyzes if a paper is relevant for a given research topic or not

# Before getting started: First of all, you need to ensure an access to Scopus API via pybliometrics: From d3ed2418c02e932147f178ac993b33f345ae5ca3 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 9 Jan 2023 22:44:06 +0100 Subject: [PATCH 09/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8698af3..349b846 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ Note: In additon to this excel file, Python generates npy files with the list of ## Python workflow: how does it work ![Python_workflow](https://user-images.githubusercontent.com/73365375/211413581-1a489dd0-7a07-4950-8a28-06523674b201.png) -

Figure 4 - How python tool analyzes if a paper is relevant for a given research topic or not

+

Figure 4 - Workflow of how a paper population is reconstructed inside of the python tool

# Before getting started: First of all, you need to ensure an access to Scopus API via pybliometrics: From 014179a8a286974e1d695141bc0e7dcad83f9345 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 9 Jan 2023 22:53:31 +0100 Subject: [PATCH 10/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 349b846..ea81e52 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ Output:

Figure 1 - Input and outputs of Python module

-## 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 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) From 5e70d8f1a4ebccae488743c6be0ae810635a41a1 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 9 Jan 2023 23:29:15 +0100 Subject: [PATCH 11/18] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index ea81e52..480a96d 100644 --- a/README.md +++ b/README.md @@ -66,3 +66,8 @@ 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 _outputs.xlsx and/or interactive graph +# Quick start: +![Python code](https://user-images.githubusercontent.com/73365375/211420715-443bd84d-c3ea-468c-965f-fb653241b07f.png) +

Figure 5 - The only input data to be changed in order to run your case in main_test.py

+ + From fa91876370833148f2254512d57f82ec86e7e2ac Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Mon, 9 Jan 2023 23:31:16 +0100 Subject: [PATCH 12/18] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 480a96d..5c47d32 100644 --- a/README.md +++ b/README.md @@ -67,6 +67,7 @@ Using a poetry to install all neccesary packages and run a code 9. After the message <<<< Analysis is finished >>>>, check the resuts in the excel file _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 ![Python code](https://user-images.githubusercontent.com/73365375/211420715-443bd84d-c3ea-468c-965f-fb653241b07f.png)

Figure 5 - The only input data to be changed in order to run your case in main_test.py

From b40413629df63d63718e759e3ccf721f9068756f Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Tue, 10 Jan 2023 13:27:40 +0100 Subject: [PATCH 13/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5c47d32..08b89d6 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ After processing your query, Python generates a excel file with papers correspon 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/73365375/211413581-1a489dd0-7a07-4950-8a28-06523674b201.png) +![Python_workflow](https://user-images.githubusercontent.com/73365375/211551610-72db9736-9168-4472-aba5-5ccf74218983.png)

Figure 4 - Workflow of how a paper population is reconstructed inside of the python tool

# Before getting started: From df91dbecf6a070565b0abf622e61286811156cc0 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Sat, 14 Jan 2023 10:23:37 +0100 Subject: [PATCH 14/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 08b89d6..7036665 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ After processing your query, Python generates a excel file with papers correspon 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/73365375/211551610-72db9736-9168-4472-aba5-5ccf74218983.png) +![Python_workflow](https://user-images.githubusercontent.com/73365375/212465231-c2ff4e45-8f3d-4970-9d92-caaf4c928145.png)

Figure 4 - Workflow of how a paper population is reconstructed inside of the python tool

# Before getting started: From 7d59118bf59ff8cd9dfa5ef7fb1d35cf3e987b40 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Sat, 14 Jan 2023 10:34:26 +0100 Subject: [PATCH 15/18] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7036665..f50fd11 100644 --- a/README.md +++ b/README.md @@ -67,8 +67,10 @@ Using a poetry to install all neccesary packages and run a code 9. After the message <<<< Analysis is finished >>>>, check the resuts in the excel file _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 +Once you installed everything, you can simply change the input data (see Figure 5) and run your case studies. The eid of your reference paper you may find on the Scopus webpage of the article (see example on Figure 6). ![Python code](https://user-images.githubusercontent.com/73365375/211420715-443bd84d-c3ea-468c-965f-fb653241b07f.png)

Figure 5 - The only input data to be changed in order to run your case in main_test.py

+![Scopus eid](https://user-images.githubusercontent.com/73365375/212465562-7d27ab6f-8ebc-4093-a532-dfa05a98c8ff.png) +

Figure 6 - The way how you may find the Scopus eid (e.g. '2-s2.0-85101235827').

From 197f02468cfbeece9ba24610d47060c4e2be25e7 Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Sat, 14 Jan 2023 10:35:14 +0100 Subject: [PATCH 16/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f50fd11..08617b3 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,6 @@ Once you installed everything, you can simply change the input data (see Figure ![Python code](https://user-images.githubusercontent.com/73365375/211420715-443bd84d-c3ea-468c-965f-fb653241b07f.png)

Figure 5 - The only input data to be changed in order to run your case in main_test.py

-![Scopus eid](https://user-images.githubusercontent.com/73365375/212465562-7d27ab6f-8ebc-4093-a532-dfa05a98c8ff.png) + ![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').

From e65e2da77859938a6f2e7e1d39f308c0c9eebe9c Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Sat, 14 Jan 2023 12:57:36 +0100 Subject: [PATCH 17/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 08617b3..63f42ae 100644 --- a/README.md +++ b/README.md @@ -72,5 +72,5 @@ Once you installed everything, you can simply change the input data (see Figure

Figure 5 - The only input data to be changed in order to run your case in main_test.py

![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').

+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). From 64f94fd576dccf316a44ac7c91dc6e7b37bfa57a Mon Sep 17 00:00:00 2001 From: Ildar DAMINOV <73365375+Ildar-Daminov@users.noreply.github.com> Date: Sat, 14 Jan 2023 17:15:21 +0100 Subject: [PATCH 18/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 63f42ae..23ce521 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ Using a poetry to install all neccesary packages and run a code 9. After the message <<<< Analysis is finished >>>>, check the resuts in the excel file _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. The eid of your reference paper you may find on the Scopus webpage of the article (see example on Figure 6). +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)

Figure 5 - The only input data to be changed in order to run your case in main_test.py