From 250088e8c00cc3c80e747f3c909128b8d7fa068e Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:21:47 -0600 Subject: [PATCH 1/6] fix conflicts --- .github/workflows/qiita-plugin-ci.yml | 52 +++++++++++++++++++++++++++ .travis.yml | 21 ----------- 2 files changed, 52 insertions(+), 21 deletions(-) create mode 100644 .github/workflows/qiita-plugin-ci.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml new file mode 100644 index 0000000..1cd7c90 --- /dev/null +++ b/.github/workflows/qiita-plugin-ci.yml @@ -0,0 +1,52 @@ +# name: qiita-files CI + +on: + push: + branches: [ dev ] + pull_request: + +jobs: + # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml + main: + runs-on: ubuntu-latest + + steps: + # Downloads a copy of the code in your repository before running CI tests + - name: Check out repository code + uses: actions/checkout@v2 + + - name: Setup for conda + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: 3.6 + + - name: Basic dependencies install + shell: bash -l {0} + run: | + + conda create --yes -n qiita-files python=$PYTHON_VERSION h5py pandas scipy numpy + conda activate qiita-files + travis_retry pip install . + + - name: Main tests + shell: bash -l {0} + run: | + conda activate qiita-files + nosetests --with-doctest --with-coverage --cover-package=qiita_files + + lint: + runs-on: ubuntu-latest + steps: + - name: flake8 + uses: actions/setup-python@v2 + with: + python-version: 3.6 + - name: install dependencies + run: python -m pip install --upgrade pip + - name: Check out repository code + uses: actions/checkout@v2 + - name: lint + run: | + pip install -q flake8 + flake8 qiita_files setup.py diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 74e1029..0000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -language: python -sudo: false -env: - - PYTHON_VERSION=3.5 - - PYTHON_VERSION=3.6 -before_install: - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh - - chmod +x miniconda.sh - - ./miniconda.sh -b - - export PATH=/home/travis/miniconda3/bin:$PATH - # Update conda itself - - conda update --yes conda -install: - - travis_retry conda create --yes -n env_name python=$PYTHON_VERSION pip nose flake8 coverage 'h5py>=2.3.1' 'pandas>=0.18' 'scipy>0.13.0' 'numpy>=1.7' - - source activate env_name - - travis_retry pip install . -script: - - nosetests --with-doctest --with-coverage --cover-package=qiita_files - - flake8 qiita_files setup.py -after_success: - - coveralls From a66df3101ce22a88f6427f0115b841cbe9c8fea7 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:24:32 -0600 Subject: [PATCH 2/6] set python-version --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 1cd7c90..b5ad8a2 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -25,7 +25,7 @@ jobs: shell: bash -l {0} run: | - conda create --yes -n qiita-files python=$PYTHON_VERSION h5py pandas scipy numpy + conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy conda activate qiita-files travis_retry pip install . From 6c861dadf3c38fa0814e85a1d0d997ecaef0d282 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:25:14 -0600 Subject: [PATCH 3/6] indent --- .github/workflows/qiita-plugin-ci.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index b5ad8a2..ffb6d77 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -24,10 +24,9 @@ jobs: - name: Basic dependencies install shell: bash -l {0} run: | - - conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy - conda activate qiita-files - travis_retry pip install . + conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy + conda activate qiita-files + travis_retry pip install . - name: Main tests shell: bash -l {0} From 20eb0b46f032407b5b826725be008cf41ddcbb10 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:30:13 -0600 Subject: [PATCH 4/6] rm travis_retry --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index ffb6d77..b8abc8e 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -26,7 +26,7 @@ jobs: run: | conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy conda activate qiita-files - travis_retry pip install . + pip install . - name: Main tests shell: bash -l {0} From 07dd806a0646da671b357e07a649ec9d50eed82c Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:38:49 -0600 Subject: [PATCH 5/6] install nosetests --- .github/workflows/qiita-plugin-ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index b8abc8e..99949d8 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -32,6 +32,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita-files + pip install nosetests nosetests --with-doctest --with-coverage --cover-package=qiita_files lint: From 20a5a103c4416ed307d190702188d3cf2a456d5c Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 16 May 2022 11:42:50 -0600 Subject: [PATCH 6/6] fix install --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 99949d8..0050431 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -27,12 +27,12 @@ jobs: conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy conda activate qiita-files pip install . + pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click - name: Main tests shell: bash -l {0} run: | conda activate qiita-files - pip install nosetests nosetests --with-doctest --with-coverage --cover-package=qiita_files lint: