From b70b80961c90c10795537566f0c0a15073d8310a Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:16:57 +0200 Subject: [PATCH 01/12] Create rst-linter.yml --- .github/workflows/rst-linter.yml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .github/workflows/rst-linter.yml diff --git a/.github/workflows/rst-linter.yml b/.github/workflows/rst-linter.yml new file mode 100644 index 00000000..fe7129e4 --- /dev/null +++ b/.github/workflows/rst-linter.yml @@ -0,0 +1,20 @@ +name: Lint + +on: + push: + pull_request: + +jobs: + doctor-rst: + name: DOCtor-RST + runs-on: ubuntu-latest + steps: + - name: "Checkout code" + uses: actions/checkout@v4 + + - name: DOCtor-RST + uses: docker://oskarstark/doctor-rst + with: + args: --short --error-format=github + env: + DOCS_DIR: 'doc/' From 3f0f49777a9b06145cfd99e8c85a589dacd6cee5 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:39:06 +0200 Subject: [PATCH 02/12] Create .doctor-rst.yaml --- doc/.doctor-rst.yaml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 doc/.doctor-rst.yaml diff --git a/doc/.doctor-rst.yaml b/doc/.doctor-rst.yaml new file mode 100644 index 00000000..18d0a309 --- /dev/null +++ b/doc/.doctor-rst.yaml @@ -0,0 +1,2 @@ +rules: + blank_line_after_directive: ~ From 5776948eee7c56391ab666290626548da9287698 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:45:26 +0200 Subject: [PATCH 03/12] Update rst-linter.yml --- .github/workflows/rst-linter.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rst-linter.yml b/.github/workflows/rst-linter.yml index fe7129e4..34d5e184 100644 --- a/.github/workflows/rst-linter.yml +++ b/.github/workflows/rst-linter.yml @@ -2,7 +2,7 @@ name: Lint on: push: - pull_request: + paths: ['**/**.rst'] jobs: doctor-rst: From fe7c324cc87cee62faf16a0b94aaead7069aee13 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:46:06 +0200 Subject: [PATCH 04/12] Update rst-linter.yml --- .github/workflows/rst-linter.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/rst-linter.yml b/.github/workflows/rst-linter.yml index 34d5e184..76020995 100644 --- a/.github/workflows/rst-linter.yml +++ b/.github/workflows/rst-linter.yml @@ -2,7 +2,6 @@ name: Lint on: push: - paths: ['**/**.rst'] jobs: doctor-rst: From 49328cba14d30437d33b7f3df8815e2e890ff369 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:47:33 +0200 Subject: [PATCH 05/12] Update changelog.rst --- doc/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/changelog.rst b/doc/changelog.rst index f8a638f4..8f90c0c2 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -3,6 +3,7 @@ Changelog .. changelog:: + :github: https://github.com/nuclear-multimessenger-astronomy/nmma/releases/ :pypi: https://pypi.org/project/nmma/ :changelog-url: https://nuclear-multimessenger-astronomy.github.io/nmma/changelog.html From 6cc436f23bcff99ebff674296a9dabda22e757c9 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:47:53 +0200 Subject: [PATCH 06/12] Update changelog.rst --- doc/changelog.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/changelog.rst b/doc/changelog.rst index 8f90c0c2..f8a638f4 100644 --- a/doc/changelog.rst +++ b/doc/changelog.rst @@ -3,7 +3,6 @@ Changelog .. changelog:: - :github: https://github.com/nuclear-multimessenger-astronomy/nmma/releases/ :pypi: https://pypi.org/project/nmma/ :changelog-url: https://nuclear-multimessenger-astronomy.github.io/nmma/changelog.html From bdfffb8a43fa8bb35ad5d58c31475cc793d4883f Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:49:48 +0200 Subject: [PATCH 07/12] Update index.rst --- doc/index.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/index.rst b/doc/index.rst index 815ae78a..1550c7b7 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -208,6 +208,7 @@ requirements.txt file which are necessary for NMMA: If everything has gone smoothly, all of these above mentioned "pip install something" commands will show that the requirements have already been satisfied. Otherwise, these will cover the dependencies if not covered by ``pip install .``. Also, if running ``pip install .`` shows something on the lines of "cannot cythonize without cython", do: .. code:: + conda install -c anaconda cython==0.29.24 pip install @@ -415,12 +416,14 @@ Internetless Clusters Some cluster resources may not have access to the internet or could block some forms of data transfer. This will cause some difficulties with certain packages and will require some fixes to how NMMA interacts with them and changes to how you call some commands in NMMA. This can also affect how you install NMMA on the cluster. Because the cluster is in some way restricted, it may be that the `conda install nmma -c conda-forge` or the `pip install nmma` commands don't work. Thus to install NMMA, you will need to install from the source. To begin, you will want to copy the NMMA repository from your local to the cluster using an `scp` or `rsync` commmand because likely the git commands will fail. Once NMMA is downloaded to the cluster, navigate to the main directory and run .. code:: + pip install -r requirements.txt pip install . and check that the installation was successful by running the first check for NMMA given above. After installation, the next most likely difference is how NMMA uses the trained kilonova models during any form of EM analysis. When running any analysis that requires the use of the trained grid of models you will need to add the `--local-only` flag to the analysis command. For example, .. code:: + lightcurve-analysis \ --model LANLTP2 \ --svd-path svdmodels/ \ From ee166ccf0e9817097d49657aef29b38cd8d9a019 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 21:53:45 +0200 Subject: [PATCH 08/12] Update .doctor-rst.yaml --- doc/.doctor-rst.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/.doctor-rst.yaml b/doc/.doctor-rst.yaml index 18d0a309..45681571 100644 --- a/doc/.doctor-rst.yaml +++ b/doc/.doctor-rst.yaml @@ -1,2 +1,5 @@ rules: blank_line_after_directive: ~ +exclude_rule_for_file: + - path: doc/changelog.rst + rule_name: blank_line_after_directive From f41f361a56da00f0f978e51a7d9284132632786f Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 22:04:28 +0200 Subject: [PATCH 09/12] Update .doctor-rst.yaml --- doc/.doctor-rst.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/.doctor-rst.yaml b/doc/.doctor-rst.yaml index 45681571..69d433bd 100644 --- a/doc/.doctor-rst.yaml +++ b/doc/.doctor-rst.yaml @@ -1,5 +1,4 @@ rules: - blank_line_after_directive: ~ + blank_line_after_directive: exclude_rule_for_file: - path: doc/changelog.rst - rule_name: blank_line_after_directive From 8cd58f02ec88aacc0f2f37e657c978a3a7f52d94 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 22:06:18 +0200 Subject: [PATCH 10/12] Update .doctor-rst.yaml --- doc/.doctor-rst.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/.doctor-rst.yaml b/doc/.doctor-rst.yaml index 69d433bd..075d974e 100644 --- a/doc/.doctor-rst.yaml +++ b/doc/.doctor-rst.yaml @@ -1,4 +1,5 @@ rules: - blank_line_after_directive: + blank_line_after_directive: ~ exclude_rule_for_file: - - path: doc/changelog.rst + - path: changelog.rst + rule_name: blank_line_after_directive From 34413b8ca13db4b61c4667cff47ad57e15cc0a75 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 22:09:28 +0200 Subject: [PATCH 11/12] Update rst-linter.yml --- .github/workflows/rst-linter.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/rst-linter.yml b/.github/workflows/rst-linter.yml index 76020995..795607e3 100644 --- a/.github/workflows/rst-linter.yml +++ b/.github/workflows/rst-linter.yml @@ -1,7 +1,8 @@ -name: Lint +name: Lint rst on: push: + paths: ['**/**.rst'] jobs: doctor-rst: From 68ddb01413ca8aa55772c1bf1e83704717cd94f5 Mon Sep 17 00:00:00 2001 From: sahiljhawar <55475299+sahiljhawar@users.noreply.github.com> Date: Fri, 5 Apr 2024 22:17:02 +0200 Subject: [PATCH 12/12] Update rst-linter.yml --- .github/workflows/rst-linter.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/rst-linter.yml b/.github/workflows/rst-linter.yml index 795607e3..ba2a7fcc 100644 --- a/.github/workflows/rst-linter.yml +++ b/.github/workflows/rst-linter.yml @@ -3,6 +3,8 @@ name: Lint rst on: push: paths: ['**/**.rst'] + pull_request: + paths: ['**/**.rst'] jobs: doctor-rst: