From 671595011cc613e419a5f5b51559fc39cc489b80 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Cl=C3=A9net?= Date: Fri, 22 Sep 2023 16:05:41 +0200 Subject: [PATCH] [DOC] fix some broken links --- docs/ci-cd.md | 2 +- docs/data.md | 2 +- docs/pipelines.md | 4 ++-- docs/running.md | 2 +- docs/testing.md | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/ci-cd.md b/docs/ci-cd.md index c292eed1..ad3f33bc 100644 --- a/docs/ci-cd.md +++ b/docs/ci-cd.md @@ -35,7 +35,7 @@ For now, the following workflows are set up: | Name / File | What does it do ? | When is it launched ? | Where does it run ? | How can I see the results ? | | ----------- | ----------- | ----------- | ----------- | ----------- | | [code_quality](/.github/workflows/code_quality.yml) | A static analysis of the python code (see the [testing](/docs/testing.md) topic of the documentation for more information). | For every push or pull_request if there are changes on `.py` files. | On GitHub servers. | Outputs (logs of pylint) are stored as [downloadable artifacts](https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts) during 15 days after the push. | -| [codespell](/.github/workflows/codespell.yml) | A static analysis of the text files for commonly made typos using [codespell](codespell-project/codespell: check code for common misspellings). | For every push or pull_request to the `maint` branch. | On GitHub servers. | Outputs (logs of codespell) are stored as [downloadable artifacts](https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts) during 15 days after the push. | +| [codespell](/.github/workflows/codespell.yml) | A static analysis of the text files for commonly made typos using [codespell](https://github.com/codespell-project/codespell). | For every push or pull_request to the `maint` branch. | On GitHub servers. | Outputs (logs of codespell) are stored as [downloadable artifacts](https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts) during 15 days after the push. | | [pipeline_tests](/.github/workflows/pipelines.yml) | Runs all the tests for changed pipelines. | For every push or pull_request, if a pipeline file changed. | On Empenn runners. | Outputs (logs of pytest) are stored as downloadable artifacts during 15 days after the push. | | [test_changes](/.github/workflows/test_changes.yml) | It runs all the changed tests for the project. | For every push or pull_request, if a test file changed. | On Empenn runners. | Outputs (logs of pytest) are stored as downloadable artifacts during 15 days after the push. | | [unit_testing](/.github/workflows/unit_testing.yml) | It runs all the unit tests for the project (see the [testing](/docs/testing.md) topic of the documentation for more information). | For every push or pull_request, if a file changed inside `narps_open/`, or a file related to test execution. | On GitHub servers. | Outputs (logs of pytest) are stored as downloadable artifacts during 15 days after the push. | diff --git a/docs/data.md b/docs/data.md index 1e6b4fc3..edf5a757 100644 --- a/docs/data.md +++ b/docs/data.md @@ -2,7 +2,7 @@ The datasets used for the project can be downloaded using one of the two options below. -The path to these datasets must conform with the information located in the configuration file you plan to use (cf. [documentation about configuration](docs/configuration.md)). By default, these paths are in the repository: +The path to these datasets must conform with the information located in the configuration file you plan to use (cf. [documentation about configuration](/docs/configuration.md)). By default, these paths are in the repository: * `data/original/`: original data from NARPS * `data/results/`: results from NARPS teams diff --git a/docs/pipelines.md b/docs/pipelines.md index fb7d2afc..db60c831 100644 --- a/docs/pipelines.md +++ b/docs/pipelines.md @@ -126,6 +126,6 @@ As explained before, all pipeline inherit from the `narps_open.pipelines.Pipelin ## Test your pipeline -First have a look at the [testing topic of the documentation](./docs/testing.md). It explains how testing works for inside project and how you should write the tests related to your pipeline. +First have a look at the [testing topic of the documentation](/docs/testing.md). It explains how testing works for inside project and how you should write the tests related to your pipeline. -Feel free to have a look at [tests/pipelines/test_team_2T6S.py](./tests/pipelines/test_team_2T6S.py), which is the file containing all the automatic tests for the 2T6S pipeline : it gives a good example. +Feel free to have a look at [tests/pipelines/test_team_2T6S.py](/tests/pipelines/test_team_2T6S.py), which is the file containing all the automatic tests for the 2T6S pipeline : it gives a good example. diff --git a/docs/running.md b/docs/running.md index 6344c042..6bc15647 100644 --- a/docs/running.md +++ b/docs/running.md @@ -61,4 +61,4 @@ python narps_open/runner.py -t 2T6S -r 4 -f python narps_open/runner.py -t 2T6S -r 4 -f -c # Check the output files without launching the runner ``` -In this usecase, the paths where to store the outputs and to the dataset are picked by the runner from the [configuration](docs/configuration.md). +In this usecase, the paths where to store the outputs and to the dataset are picked by the runner from the [configuration](/docs/configuration.md). diff --git a/docs/testing.md b/docs/testing.md index 2bd96584..5294ea9b 100644 --- a/docs/testing.md +++ b/docs/testing.md @@ -55,7 +55,7 @@ Use pytest [markers](https://docs.pytest.org/en/7.1.x/example/markers.html) to i | Type of test | marker | Description | | ----------- | ----------- | ----------- | | unit tests | `unit_test` | Unitary test a method/function | -| pipeline tests | `pieline_test` | Compute a whole pipeline and check its outputs are close enough with the team's results | +| pipeline tests | `pipeline_test` | Compute a whole pipeline and check its outputs are close enough with the team's results | ## Save time by downsampling data