From f5f7d518746af374c227ce6dbc2984b474694494 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Pedersen?= Date: Thu, 10 Aug 2023 12:01:10 +0200 Subject: [PATCH] Added two new notebooks + added respective CIs and updated README --- .github/workflows/incidence_mortality_age.yml | 32 +++++++++++++++++++ .github/workflows/incidence_temporal_age.yml | 32 +++++++++++++++++++ README.md | 8 +++-- 3 files changed, 69 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/incidence_mortality_age.yml create mode 100644 .github/workflows/incidence_temporal_age.yml diff --git a/.github/workflows/incidence_mortality_age.yml b/.github/workflows/incidence_mortality_age.yml new file mode 100644 index 0000000..1f52ca4 --- /dev/null +++ b/.github/workflows/incidence_mortality_age.yml @@ -0,0 +1,32 @@ +name: mortality_temporal_age + +on: + push: + branches: + - '*' + pull_request: + branches: + - '*' + workflow_dispatch: + +jobs: + notebooks: + runs-on: ubuntu-20.04 + steps: + - uses: actions/checkout@v1 + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - name: Install dependencies + run: pip install jupyter nbconvert nbformat + + - name: Launch notebook + run: jupyter nbconvert --to notebook --execute apps/bc_mortality_over_time_age_groups.ipynb --ExecutePreprocessor.kernel_name='python3' --output ../notebook_executed + + - name: Upload artifact + uses: actions/upload-artifact@v3 + with: + name: notebook + path: notebook_executed.ipynb diff --git a/.github/workflows/incidence_temporal_age.yml b/.github/workflows/incidence_temporal_age.yml new file mode 100644 index 0000000..aa32cb1 --- /dev/null +++ b/.github/workflows/incidence_temporal_age.yml @@ -0,0 +1,32 @@ +name: incidence_temporal_age + +on: + push: + branches: + - '*' + pull_request: + branches: + - '*' + workflow_dispatch: + +jobs: + notebooks: + runs-on: ubuntu-20.04 + steps: + - uses: actions/checkout@v1 + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 + + - name: Install dependencies + run: pip install jupyter nbconvert nbformat + + - name: Launch notebook + run: jupyter nbconvert --to notebook --execute apps/bc_incidence_over_time_age_groups.ipynb --ExecutePreprocessor.kernel_name='python3' --output ../notebook_executed + + - name: Upload artifact + uses: actions/upload-artifact@v3 + with: + name: notebook + path: notebook_executed.ipynb diff --git a/README.md b/README.md index 6cf1e76..86dc8bc 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,8 @@ They can also be accessed by clicking their respective CoLab badge below: | Survival country comparison | Open In Colab | Open In Colab | | Cancer incidence over time | Open In Colab | Open In Colab | | Cancer mortality over time | Open In Colab | Open In Colab | +| Cancer incidence over time w.r.t age | Open In Colab | Open In Colab | +| Cancer mortality over time w.r.t age | Open In Colab | Open In Colab | ## [Dependencies](https://github.com/andreped/breast-cancer-stats#dependencies) @@ -42,9 +44,9 @@ The following dependencies were used and are installed as part of the notebooks: ## [Troubleshooting](https://github.com/andreped/breast-cancer-stats#troubleshooting) -If you attempt to run the notebooks locally or view them from GitHub, the resulting image may not be displayed. -This is due to the renderer in Plotly's `show()` method being set to `show(renderer="colab")`. -By removing the specification of renderer or choosing an appropriate renderer, the resulting image should be shown in the notebook. +Note that all renderered results could be interactive, but we have set Plotly's `show(renderer="png")`, +to enable the result to be shown in the output on CoLab, on GitHub, and locally. To get interactive +figures on CoLab set `show(renderer="colab")`, or locally use the default `show()`. ## [License](https://github.com/andreped/breast-cancer-stats#license)