From ec877e37c313904caf58c0adbd2656ee86dddad7 Mon Sep 17 00:00:00 2001 From: Kaivan Kamali Date: Thu, 7 Oct 2021 10:27:33 -0400 Subject: [PATCH 1/4] Added documentation on how to run the tests --- README.rst | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/README.rst b/README.rst index 5959b5925..69eee6fa9 100644 --- a/README.rst +++ b/README.rst @@ -25,3 +25,33 @@ overview also available in `ABOUT.rst <./ABOUT.rst>`_. .. References/hyperlinks used above .. _CloudMan: https://galaxyproject.org/cloudman/ .. _Galaxy: https://galaxyproject.org/ + +How to run BioBlend tests +************************* + +1. Clone galaxy in ~ via `git clone https://github.com/galaxyproject/galaxy.git` +2. Copy sample galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml` +3. Open ~/galaxy/config/galaxy.yml in an editor, uncomment `master_api_key` line, set it to a value, and save your change +4. Start galaxy by running `~/galaxy/run.sh` +5. In a browser, type `127.0.0.1:8080` and login to galaxy by clicking on `Login or Register +6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value +7. Clone bioblend in ~ via `git clone https://github.com/galaxyproject/bioblend` +8. Set the following environment variables by running these commands in a terminal. Use master API key in step 3, your login email in step 6, and API key in step 7. Change galaxy version and job timeout, if needed + + * `export BIOBLEND_GALAXY_API_KEY=` + + * `export BIOBLEND_GALAXY_MASTER_API_KEY=` + + * `export BIOBLEND_GALAXY_URL=http://127.0.01:8080` + + * `export BIOBLEND_GALAXY_USER_EMAIL=` + + * `export BIOBLEND_TEST_JOB_TIMEOUT=100` + + * `export GALAXY_VERSION=21.09` + +9. Run bioblend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt` + + * Pass your machine's Python version via `-e` flag. E.g., pass `py39` for Python 3.9 + + * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt From 387235cfa3bc65d8c1dc46a85c5c72f32c6d72c3 Mon Sep 17 00:00:00 2001 From: Kaivan Kamali Date: Thu, 14 Oct 2021 08:52:49 -0400 Subject: [PATCH 2/4] Moved documentation to run tests from readme to contributing file --- CONTRIBUTING.md | 30 ++++++++++++++++++++++++++++++ README.rst | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 68e20d070..65c81d909 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -7,3 +7,33 @@ Making a new release 4. Commit the changes above, push to GitHub, and wait for Continuous Integration (CI) tests to pass. 5. Make a new release through the GitHub interface. A CI job will automatically upload the packages to PyPI. 7. Optionally update the [Bioconda package](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioblend/meta.yaml). + +How to run BioBlend tests +------------------------- + +1. Clone galaxy in ~ via `git clone https://github.com/galaxyproject/galaxy.git` +2. Copy sample galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml` +3. Open ~/galaxy/config/galaxy.yml in an editor, uncomment `master_api_key` line, set it to a value, and save your change +4. Start galaxy by running `~/galaxy/run.sh` +5. In a browser, type `127.0.0.1:8080` and login to galaxy by clicking on `Login or Register` +6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value +7. Clone bioblend in ~ via `git clone https://github.com/galaxyproject/bioblend` +8. Set the following environment variables by running these commands in a terminal. Use master API key in step 3, your login email in step 6, and API key in step 7. Change galaxy version and job timeout, if needed + + * `export BIOBLEND_GALAXY_API_KEY=` + + * `export BIOBLEND_GALAXY_MASTER_API_KEY=` + + * `export BIOBLEND_GALAXY_URL=http://127.0.01:8080` + + * `export BIOBLEND_GALAXY_USER_EMAIL=` + + * `export BIOBLEND_TEST_JOB_TIMEOUT=100` + + * `export GALAXY_VERSION=21.09` + +9. Run bioblend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt` + + * Pass your machine's Python version via `-e` flag. E.g., pass `py39` for Python 3.9 + + * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt diff --git a/README.rst b/README.rst index 69eee6fa9..5959b5925 100644 --- a/README.rst +++ b/README.rst @@ -25,33 +25,3 @@ overview also available in `ABOUT.rst <./ABOUT.rst>`_. .. References/hyperlinks used above .. _CloudMan: https://galaxyproject.org/cloudman/ .. _Galaxy: https://galaxyproject.org/ - -How to run BioBlend tests -************************* - -1. Clone galaxy in ~ via `git clone https://github.com/galaxyproject/galaxy.git` -2. Copy sample galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml` -3. Open ~/galaxy/config/galaxy.yml in an editor, uncomment `master_api_key` line, set it to a value, and save your change -4. Start galaxy by running `~/galaxy/run.sh` -5. In a browser, type `127.0.0.1:8080` and login to galaxy by clicking on `Login or Register -6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value -7. Clone bioblend in ~ via `git clone https://github.com/galaxyproject/bioblend` -8. Set the following environment variables by running these commands in a terminal. Use master API key in step 3, your login email in step 6, and API key in step 7. Change galaxy version and job timeout, if needed - - * `export BIOBLEND_GALAXY_API_KEY=` - - * `export BIOBLEND_GALAXY_MASTER_API_KEY=` - - * `export BIOBLEND_GALAXY_URL=http://127.0.01:8080` - - * `export BIOBLEND_GALAXY_USER_EMAIL=` - - * `export BIOBLEND_TEST_JOB_TIMEOUT=100` - - * `export GALAXY_VERSION=21.09` - -9. Run bioblend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt` - - * Pass your machine's Python version via `-e` flag. E.g., pass `py39` for Python 3.9 - - * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt From 1ea27566a486d3825a6f3b7462a80b63169e5807 Mon Sep 17 00:00:00 2001 From: Simon Bray Date: Thu, 21 Oct 2021 17:00:17 +0200 Subject: [PATCH 3/4] small changes to instructions for running tests --- CONTRIBUTING.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 65c81d909..270e597bd 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,19 +6,19 @@ Making a new release 3. Update `CHANGELOG.md` . 4. Commit the changes above, push to GitHub, and wait for Continuous Integration (CI) tests to pass. 5. Make a new release through the GitHub interface. A CI job will automatically upload the packages to PyPI. -7. Optionally update the [Bioconda package](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioblend/meta.yaml). +7. Update the [Bioconda package](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioblend/meta.yaml). How to run BioBlend tests ------------------------- -1. Clone galaxy in ~ via `git clone https://github.com/galaxyproject/galaxy.git` -2. Copy sample galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml` -3. Open ~/galaxy/config/galaxy.yml in an editor, uncomment `master_api_key` line, set it to a value, and save your change -4. Start galaxy by running `~/galaxy/run.sh` -5. In a browser, type `127.0.0.1:8080` and login to galaxy by clicking on `Login or Register` -6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value -7. Clone bioblend in ~ via `git clone https://github.com/galaxyproject/bioblend` -8. Set the following environment variables by running these commands in a terminal. Use master API key in step 3, your login email in step 6, and API key in step 7. Change galaxy version and job timeout, if needed +1. Clone Galaxy via `git clone https://github.com/galaxyproject/galaxy.git`. +2. Copy the sample Galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml`. +3. Open `galaxy/config/galaxy.yml` in an editor, uncomment the `master_api_key` line, set it to a value, and save your change. +4. Start Galaxy by running `./galaxy/run.sh`. +5. In a browser, type `127.0.0.1:8080` to go to the Galaxy server and login by clicking on `Login or Register`. +6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value. +7. Clone BioBlend via `git clone https://github.com/galaxyproject/bioblend`. +8. Set the following environment variables by running these commands in a terminal. Use the master API key set in step 3, your login email from step 6, and the API key obtained in step 7. Change the Galaxy version and job timeout, if needed. * `export BIOBLEND_GALAXY_API_KEY=` @@ -32,8 +32,8 @@ How to run BioBlend tests * `export GALAXY_VERSION=21.09` -9. Run bioblend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt` +9. Run BioBlend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt`. - * Pass your machine's Python version via `-e` flag. E.g., pass `py39` for Python 3.9 + * Pass your machine's Python version via `-e` flag. E.g. pass `py39` for Python 3.9. - * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt + * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt. From b4b2928d66eda5c2d8746a239208dcf6f08ffd30 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 16 Jun 2023 12:36:16 +0100 Subject: [PATCH 4/4] Update BioBlend testing howto --- CONTRIBUTING.md | 29 +++++------------------------ 1 file changed, 5 insertions(+), 24 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 270e597bd..999eb1026 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,34 +6,15 @@ Making a new release 3. Update `CHANGELOG.md` . 4. Commit the changes above, push to GitHub, and wait for Continuous Integration (CI) tests to pass. 5. Make a new release through the GitHub interface. A CI job will automatically upload the packages to PyPI. -7. Update the [Bioconda package](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioblend/meta.yaml). +7. Check and merge the automatic pull request to update the [Bioconda package](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioblend/meta.yaml). How to run BioBlend tests ------------------------- -1. Clone Galaxy via `git clone https://github.com/galaxyproject/galaxy.git`. -2. Copy the sample Galaxy config file via `cp ~/galaxy/config/galaxy.yml.sample ~/galaxy/config/galaxy.yml`. -3. Open `galaxy/config/galaxy.yml` in an editor, uncomment the `master_api_key` line, set it to a value, and save your change. -4. Start Galaxy by running `./galaxy/run.sh`. -5. In a browser, type `127.0.0.1:8080` to go to the Galaxy server and login by clicking on `Login or Register`. -6. Select User -> Preferences -> Manage API Key. Create a new API key and save the key value. -7. Clone BioBlend via `git clone https://github.com/galaxyproject/bioblend`. -8. Set the following environment variables by running these commands in a terminal. Use the master API key set in step 3, your login email from step 6, and the API key obtained in step 7. Change the Galaxy version and job timeout, if needed. +1. Clone Galaxy to a directory outside of BioBlend source directory via `git clone https://github.com/galaxyproject/galaxy.git` - * `export BIOBLEND_GALAXY_API_KEY=` +2. Change directory to your BioBlend source and run the tests via `./run_bioblend_tests.sh -g GALAXY_PATH [-r GALAXY_REV] [-e TOX_ENV]` where `GALAXY_PATH` is the directory where the galaxy repository was cloned, `GALAXY_REV` is the branch or commit of Galaxy that you would like to test against (if different from the current state of your galaxy clone), and `TOX_ENV` is used to specify the Python version to use for BioBlend, e.g. `py37` for Python 3.7. - * `export BIOBLEND_GALAXY_MASTER_API_KEY=` + You can also add `2>&1 | tee log.txt` to the command above to contemporarily view the test output and save it to the `log.txt` file. - * `export BIOBLEND_GALAXY_URL=http://127.0.01:8080` - - * `export BIOBLEND_GALAXY_USER_EMAIL=` - - * `export BIOBLEND_TEST_JOB_TIMEOUT=100` - - * `export GALAXY_VERSION=21.09` - -9. Run BioBlend tests via `~/bioblend/run_bioblend_tests.sh -g ~/galaxy -e py39 2>&1 | tee log.txt`. - - * Pass your machine's Python version via `-e` flag. E.g. pass `py39` for Python 3.9. - - * Re-route stderr to stdout via `2>&1` and `tee` the output so you can both view it and save it to log.txt. +3. If needed, you can temporarily increase the Galaxy job timeout used by BioBlend tests with e.g. `export BIOBLEND_TEST_JOB_TIMEOUT=100`, and re-run the tests.