From b68c97885271cadd864387812b73f94b391ca4ee Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:25:38 -0400 Subject: [PATCH 01/10] Create greet.yml to test continuous integration on my repository --- .github/workflows/greet.yml | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 .github/workflows/greet.yml diff --git a/.github/workflows/greet.yml b/.github/workflows/greet.yml new file mode 100644 index 0000000..28f9f12 --- /dev/null +++ b/.github/workflows/greet.yml @@ -0,0 +1,34 @@ +# name of the workflow +name: greet + +# when the workflow should run +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +# independent jobs in the workflow +jobs: + # this workflow just has one job called "greet" + greet: + # the operating system to use for this workflow + runs-on: ubuntu-latest + # list of steps in the workflow + steps: + # use an action provided by github to checkout the repo + - uses: actions/checkout@v3 + # a custom step that runs a couple shell commands + - name: List + run: | + echo "listing files in the design_documents directory" + ls design_documents + # a custom step that runs R code + - name: Greet + run: print("Hello, world!") + # Replace `shell: Rscript {0}` with `shell: python {0}` to run Python code instead! + shell: python {0} From 47cd1dc08c43499c2df3c53e1b8d5eb718f765a4 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:29:04 -0400 Subject: [PATCH 02/10] Update greet.yml to correctly use the W24 default branch not main --- .github/workflows/greet.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/greet.yml b/.github/workflows/greet.yml index 28f9f12..1c9ee2f 100644 --- a/.github/workflows/greet.yml +++ b/.github/workflows/greet.yml @@ -5,13 +5,11 @@ name: greet on: push: branches: - - main - - master + - W24 pull_request: branches: - - main - - master - + - W24 + # independent jobs in the workflow jobs: # this workflow just has one job called "greet" From f4c4c8108df8d2b244333f640987be0d3cb31181 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:42:37 -0400 Subject: [PATCH 03/10] Create ci_test - workflow for running tests automatically --- .github/workflows/ci_test | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 .github/workflows/ci_test diff --git a/.github/workflows/ci_test b/.github/workflows/ci_test new file mode 100644 index 0000000..313c899 --- /dev/null +++ b/.github/workflows/ci_test @@ -0,0 +1,31 @@ +name: CI + +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Set up Python 3.11 + uses: actions/setup-python@v3 + with: + python-version: "3.11" + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pytest + if [ -f requirements.txt ]; then + pip install -r requirements.txt + fi + - name: Test with pytest + run: | + pytest . From 80eaf3fa240a2d10a56e4c8f066551f091bb85d9 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:46:27 -0400 Subject: [PATCH 04/10] Rename ci_test to ci_test.yml --- .github/workflows/{ci_test => ci_test.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{ci_test => ci_test.yml} (100%) diff --git a/.github/workflows/ci_test b/.github/workflows/ci_test.yml similarity index 100% rename from .github/workflows/ci_test rename to .github/workflows/ci_test.yml From 6248fb312fb628ba9a2c33034df476e6a2ab04b1 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:48:48 -0400 Subject: [PATCH 05/10] Update ci_test.yml to have the correct branch for on --- .github/workflows/ci_test.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml index 313c899..c6631de 100644 --- a/.github/workflows/ci_test.yml +++ b/.github/workflows/ci_test.yml @@ -3,12 +3,10 @@ name: CI on: push: branches: - - main - - master + - W24 pull_request: branches: - - main - - master + - W24 jobs: build: From 9de65c1c355ff8767be9f5e80b7a747046c2b282 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:52:05 -0400 Subject: [PATCH 06/10] Create example.py --- example.py | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 example.py diff --git a/example.py b/example.py new file mode 100644 index 0000000..12ce4b3 --- /dev/null +++ b/example.py @@ -0,0 +1,2 @@ +def test_add(): + assert 2 + 5 == 7 From 7c63ae8f93366aeb4dc43c1362a81dc0adc9d175 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:54:40 -0400 Subject: [PATCH 07/10] Rename example.py to TCGA_matchmaker/example.py --- example.py => TCGA_matchmaker/example.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename example.py => TCGA_matchmaker/example.py (100%) diff --git a/example.py b/TCGA_matchmaker/example.py similarity index 100% rename from example.py rename to TCGA_matchmaker/example.py From 2ea7a0ae9758844318738c674a61461ebc2bda41 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:56:46 -0400 Subject: [PATCH 08/10] Rename example.py to test_example.py --- TCGA_matchmaker/{example.py => test_example.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename TCGA_matchmaker/{example.py => test_example.py} (100%) diff --git a/TCGA_matchmaker/example.py b/TCGA_matchmaker/test_example.py similarity index 100% rename from TCGA_matchmaker/example.py rename to TCGA_matchmaker/test_example.py From 05ff5fe478e5d59e85a55b8dcdcc6b2eb9dd88b2 Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Mon, 25 Mar 2024 14:56:11 -0400 Subject: [PATCH 09/10] Rename test_example.py to pytest_example.py --- TCGA_matchmaker/{test_example.py => pytest_example.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename TCGA_matchmaker/{test_example.py => pytest_example.py} (100%) diff --git a/TCGA_matchmaker/test_example.py b/TCGA_matchmaker/pytest_example.py similarity index 100% rename from TCGA_matchmaker/test_example.py rename to TCGA_matchmaker/pytest_example.py From 44bb2ca184742c40b16ed322b1cc4fbf5222634d Mon Sep 17 00:00:00 2001 From: mitreac <53021555+mitreac@users.noreply.github.com> Date: Mon, 25 Mar 2024 15:18:57 -0400 Subject: [PATCH 10/10] Rename pytest_example.py to test_example.py --- TCGA_matchmaker/{pytest_example.py => test_example.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename TCGA_matchmaker/{pytest_example.py => test_example.py} (100%) diff --git a/TCGA_matchmaker/pytest_example.py b/TCGA_matchmaker/test_example.py similarity index 100% rename from TCGA_matchmaker/pytest_example.py rename to TCGA_matchmaker/test_example.py