diff --git a/.github/actions/test-docs/action.yml b/.github/actions/test-docs/action.yml deleted file mode 100644 index 01971cf006..0000000000 --- a/.github/actions/test-docs/action.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: "Test Doc" -description: "Create the documentation." -runs: - using: "composite" - steps: - - name: Install dependencies - shell: bash - run: | - sudo apt-get -qq update - sudo apt-get -qq -y install doxygen - - name: Create documentation - shell: bash - run: | - cd docs - doxygen - - name: Upload Documentation - uses: actions/upload-artifact@v4 - with: - name: documentation - path: docs/html - retention-days: 3 diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index da3e458a7f..efc5f5b31b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -316,13 +316,6 @@ jobs: package: surrogatemodel coverage: ON - test-docs: - if: github.event.pull_request.draft == false - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: ./.github/actions/test-docs - codecov: if: github.event.pull_request.draft == false needs: merge-test-artifacts @@ -348,71 +341,3 @@ jobs: directory: ./coverage_python files: ./coverage_python/**,./coverage.info verbose: true - - pages: - if: github.event.pull_request.draft == false - permissions: - contents: write - needs: [test-docs, merge-test-artifacts] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Install dependencies - run: | - sudo apt-get -qq update - sudo apt-get -qq -y install git - - name: Download python coverage report - uses: actions/download-artifact@v4 - with: - name: test-py-coverage-reports-surrogatemodel - - name: Download cpp coverage report - uses: actions/download-artifact@v4 - with: - name: test-cpp-coverage-reports - - name: Download pylint report - #if an error occurs here, the pylint report was not built, probably manually trigger epidata-ci - uses: dawidd6/action-download-artifact@v6 - with: - github_token: ${{secrets.GITHUB_TOKEN}} - workflow: epidata_main.yml - name: pylint-report-epidata - path: pycode/build_pylint - - name: Download documentation - uses: actions/download-artifact@v4 - with: - name: documentation - path: docs/html - - name: Prepare basic Pages sites - run: | - mkdir -p public - cp docs/style.css public/style.css - cp docs/index.html public/index.html - - name: Prepare pylint reports - run: | - mkdir -p public/pylint - cp pycode/build_pylint/pylint.html public/pylint/index.html - - name: Prepare documentation - run: | - mkdir -p public/documentation - cp -r docs/html/* public/documentation - - name: Prepare coverage reports - run: | - mkdir -p public/coverage - mkdir -p public/coverage/cpp - mkdir -p public/coverage/python - cp -r coverage_python/* public/coverage/python/ - cp -r coverage/* public/coverage/cpp/ - - name: Upload pages as artifact - uses: actions/upload-artifact@v4 - if: github.event_name == 'pull_request' && github.ref != 'refs/heads/main' - with: - name: pages - path: public - if-no-files-found: error - retention-days: 1 - - name: Deploy to gh-pages branch - uses: peaceiris/actions-gh-pages@v3 - if: github.event_name == 'push' && github.ref == 'refs/heads/main' - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./public diff --git a/docs/README.md b/docs/README.md index 366402bddc..77ca48ca99 100755 --- a/docs/README.md +++ b/docs/README.md @@ -1,8 +1,8 @@ MEmilio Documentation =============================== -The MEmilio documentation is created by [doxygen](https://www.doxygen.nl/). The documentation of the main branch is automatically deployed to https://scicompmod.github.io/memilio/documentation/index.html by the continuous integration process. +With every merged pull request, the online documentation gets updated at: [https://memilio.readthedocs.io/en/latest/](https://memilio.readthedocs.io/en/latest/). -In order to create the MEmilio documentation locally, follow the procedure below. +A MEmilio documentation can also be created locally with [doxygen](https://www.doxygen.nl/). In order to do so, follow the procedure below. How to create the documentation: --------------------------------- diff --git a/docs/index.html b/docs/index.html deleted file mode 100644 index 8cd77f4444..0000000000 --- a/docs/index.html +++ /dev/null @@ -1,146 +0,0 @@ - - - - - MEmilio - a high performance Modular EpideMIcs simuLatIOn software - - - - - - - - - - - - - - - - - - -
- -
-

MEmilio - a high performance Modular EpideMIcs simuLatIOn software

- -
- MEmilio implements various models for infectious disease dynamics, from simple compartmental models through - Integro-Differential equation-based models to agent- or individual-based models. Its modular design allows the - combination of different models with different mobility patterns. Through efficient implementation and - parallelization, MEmilio brings cutting edge and compute intensive epidemiological models to a large scale, - enabling a precise and high-resolution spatiotemporal infectious disease dynamics. MEmilio will be extended - continuously. It is available open-source and we encourage everyone to make use of it.

- - If you use MEmilio, please cite our works: - -
    -
  • Kühn, Martin Joachim und Abele, Daniel und Kerkmann, David und Korf, Sascha Alexander und Zunker, Henrik - und - Wendler, Anna Clara und Bicker, Julia und Nguyen, Dang Khoa und Klitz, Margrit und Koslow, Wadim und Siggel, - Martin und Kleinert, Jan und Rack, Kathrin und Binder, Sebastian und Plötzke, Lena und Schmieding, René und - Lenz, Patrick und Betz, Maximilian Franz und Lutz, Annette und Gerstein, Carlotta und Schmidt, Agatha und - Meyer-Hermann, Michael und Basermann, Achim (2022) MEmilio - a high performance Modular EpideMIcs simuLatIOn - software (2022). https://github.com/SciCompMod/memilio, - https://elib.dlr.de/192140/.

  • - -
  • Koslow W, Kühn MJ, Binder S, Klitz M, Abele D, et al. (2022) Appropriate relaxation of non-pharmaceutical - interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant. - PLOS - Computational Biology 18(5): e1010054. https://doi.org/10.1371/journal.pcbi.1010054
  • -
-

- - Contact: Martin.Kuehn@DLR.de -

-
- -
- -
- - - - - - - - - - \ No newline at end of file diff --git a/docs/style.css b/docs/style.css deleted file mode 100644 index 0eb21bcab5..0000000000 --- a/docs/style.css +++ /dev/null @@ -1,147 +0,0 @@ -h1 { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - letter-spacing: 1px; - line-height: 1.8em; - font-size: 20pt; - font-weight: normal; - font-style: normal; - padding-left: 12.5%; - padding-right: 12.5%; -} - -h2 { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - letter-spacing: 1px; - line-height: 1.6em; - font-size: 14pt; - font-weight: bold; - font-style: normal; - padding-left: 12.5%; - padding-right: 12.5%; -} - -h3 { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - letter-spacing: 1px; - line-height: 1.6em; - font-size: 12pt; - font-weight: bold; - font-style: normal; - padding-left: 12.5%; - padding-right: 12.5%; -} - -a:link { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 11pt; - font-weight: normal; - text-decoration: underline; -} - -a:visited { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 11pt; - font-weight: normal; - text-decoration: underline; -} - -a:active { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 11pt; - font-weight: normal; - text-decoration: underline; -} - -a:hover { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 11pt; - font-weight: normal; - text-decoration: underline; -} - -.menu { - min-width: 175px; - text-align: center; - float: left; - position: relative; - border-radius: 25px; -} - -.menu:hover { - background-color: #00abc4; -} - -.content { - background-color: #00abc4; - margin: 0px; - padding-left: 12.5%; - padding-right: 12.5%; - padding-top: 50px; - padding-bottom: 50px; - background-clip: padding-box; -} - -a.menu:link { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 14pt; - font-weight: bold; - text-decoration: none; -} - -a.menu:visited { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 14pt; - font-weight: bold; - text-decoration: none; -} - -a.menu:active { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 14pt; - font-weight: bold; - text-decoration: none; -} - -a.menu:hover { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - color: #000000; - letter-spacing: 1px; - font-size: 14pt; - font-weight: bold; - text-decoration: none; - -webkit-transition: all 0.2s linear; - -moz-transition: all 0.2s linear; - -o-transition: all 0.2s linear; - -ms-transition: all 0.2s linear; - transition: all 0.2s linear; -} - -html { - height: 100%; - width: 100%; -} - -body { - font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif; - letter-spacing: 1px; - font-size: 11pt; - line-height: 1.6em; - font-weight: normal; - margin: 0px; - padding: 0px; - height: 100%; -} \ No newline at end of file