From a3101760c1b3139d8cfda5330a7dd506dc07ceed Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 2 Jul 2024 16:36:41 -0700 Subject: [PATCH 1/6] Copy subcommand order from source MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Copied from source¹ which is the order shown in help output. ¹ augur/curate/__init__.py:SUBCOMMANDS --- docs/usage/cli/curate/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index ab8d2f0b8..1291dd355 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -16,8 +16,8 @@ We will continue to add more subcommands as we identify other common data curati .. toctree:: :maxdepth: 1 + passthru normalize-strings - titlecase format-dates - passthru + titlecase From e7ac092eec877e7275148f0bf55c727cfbba9e89 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 2 Jul 2024 17:02:36 -0700 Subject: [PATCH 2/6] Add CLI doc for augur curate apply-geolocation-rules --- docs/usage/cli/curate/apply-geolocation-rules.rst | 9 +++++++++ docs/usage/cli/curate/index.rst | 1 + 2 files changed, 10 insertions(+) create mode 100644 docs/usage/cli/curate/apply-geolocation-rules.rst diff --git a/docs/usage/cli/curate/apply-geolocation-rules.rst b/docs/usage/cli/curate/apply-geolocation-rules.rst new file mode 100644 index 000000000..fc90cd517 --- /dev/null +++ b/docs/usage/cli/curate/apply-geolocation-rules.rst @@ -0,0 +1,9 @@ +======================= +apply-geolocation-rules +======================= + +.. argparse:: + :module: augur + :func: make_parser + :prog: augur + :path: curate apply-geolocation-rules diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index 1291dd355..2ef8df6e3 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -20,4 +20,5 @@ We will continue to add more subcommands as we identify other common data curati normalize-strings format-dates titlecase + apply-geolocation-rules From 40d60a1cf46a001e743e810dc48ef521e5b85617 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 2 Jul 2024 17:05:00 -0700 Subject: [PATCH 3/6] Add CLI doc for augur curate apply-record-annotations --- docs/usage/cli/curate/apply-record-annotations.rst | 9 +++++++++ docs/usage/cli/curate/index.rst | 1 + 2 files changed, 10 insertions(+) create mode 100644 docs/usage/cli/curate/apply-record-annotations.rst diff --git a/docs/usage/cli/curate/apply-record-annotations.rst b/docs/usage/cli/curate/apply-record-annotations.rst new file mode 100644 index 000000000..0e5318bc3 --- /dev/null +++ b/docs/usage/cli/curate/apply-record-annotations.rst @@ -0,0 +1,9 @@ +======================== +apply-record-annotations +======================== + +.. argparse:: + :module: augur + :func: make_parser + :prog: augur + :path: curate apply-record-annotations diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index 2ef8df6e3..d1a25cca6 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -21,4 +21,5 @@ We will continue to add more subcommands as we identify other common data curati format-dates titlecase apply-geolocation-rules + apply-record-annotations From 3ac703a360f8b34ad563976f3c3ba8915e32fa7a Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 2 Jul 2024 17:06:53 -0700 Subject: [PATCH 4/6] Add CLI doc for augur curate abbreviate-authors --- docs/usage/cli/curate/abbreviate-authors.rst | 9 +++++++++ docs/usage/cli/curate/index.rst | 1 + 2 files changed, 10 insertions(+) create mode 100644 docs/usage/cli/curate/abbreviate-authors.rst diff --git a/docs/usage/cli/curate/abbreviate-authors.rst b/docs/usage/cli/curate/abbreviate-authors.rst new file mode 100644 index 000000000..0597b0093 --- /dev/null +++ b/docs/usage/cli/curate/abbreviate-authors.rst @@ -0,0 +1,9 @@ +================== +abbreviate-authors +================== + +.. argparse:: + :module: augur + :func: make_parser + :prog: augur + :path: curate abbreviate-authors diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index d1a25cca6..b2df47072 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -22,4 +22,5 @@ We will continue to add more subcommands as we identify other common data curati titlecase apply-geolocation-rules apply-record-annotations + abbreviate-authors From 5cfad36d17446c2a1a339e769c09b33f9448e7c6 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 2 Jul 2024 17:13:00 -0700 Subject: [PATCH 5/6] Add CLI doc for augur curate parse-genbank-location --- docs/usage/cli/curate/index.rst | 1 + docs/usage/cli/curate/parse-genbank-location.rst | 9 +++++++++ 2 files changed, 10 insertions(+) create mode 100644 docs/usage/cli/curate/parse-genbank-location.rst diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index b2df47072..4e33e5b39 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -23,4 +23,5 @@ We will continue to add more subcommands as we identify other common data curati apply-geolocation-rules apply-record-annotations abbreviate-authors + parse-genbank-location diff --git a/docs/usage/cli/curate/parse-genbank-location.rst b/docs/usage/cli/curate/parse-genbank-location.rst new file mode 100644 index 000000000..1ef23dc81 --- /dev/null +++ b/docs/usage/cli/curate/parse-genbank-location.rst @@ -0,0 +1,9 @@ +====================== +parse-genbank-location +====================== + +.. argparse:: + :module: augur + :func: make_parser + :prog: augur + :path: curate parse-genbank-location From 09e2cc6f7b48c523b6c661824f0f3e625abf5d4a Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Mon, 8 Jul 2024 11:24:45 -0700 Subject: [PATCH 6/6] Add CLI doc for augur curate transform-strain-name --- docs/usage/cli/curate/index.rst | 1 + docs/usage/cli/curate/transform-strain-name.rst | 9 +++++++++ 2 files changed, 10 insertions(+) create mode 100644 docs/usage/cli/curate/transform-strain-name.rst diff --git a/docs/usage/cli/curate/index.rst b/docs/usage/cli/curate/index.rst index 4e33e5b39..a83bd1ce3 100644 --- a/docs/usage/cli/curate/index.rst +++ b/docs/usage/cli/curate/index.rst @@ -24,4 +24,5 @@ We will continue to add more subcommands as we identify other common data curati apply-record-annotations abbreviate-authors parse-genbank-location + transform-strain-name diff --git a/docs/usage/cli/curate/transform-strain-name.rst b/docs/usage/cli/curate/transform-strain-name.rst new file mode 100644 index 000000000..b12a2cfc9 --- /dev/null +++ b/docs/usage/cli/curate/transform-strain-name.rst @@ -0,0 +1,9 @@ +===================== +transform-strain-name +===================== + +.. argparse:: + :module: augur + :func: make_parser + :prog: augur + :path: curate transform-strain-name