diff --git a/CHANGES.md b/CHANGES.md index f88715f1..d96eaead 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -13,6 +13,16 @@ development source code and as such may not be routinely kept up to date. # __NEXT__ +## Improvements + +* Added the following to the list of "well-known" environment variables that are + automatically passed thru to runtimes: + + - `AUGUR_SEARCH_PATHS` + - `AUGUR_DEBUG` + - `AUGUR_PROFILE` + + ([#501](https://github.com/nextstrain/cli/pull/501)) # 10.4.2 (7 January 2026) diff --git a/doc/changes.md b/doc/changes.md index 4ea3789a..0480819d 100644 --- a/doc/changes.md +++ b/doc/changes.md @@ -16,6 +16,17 @@ development source code and as such may not be routinely kept up to date. (v-next)= ## __NEXT__ +(v-next-improvements)= +### Improvements + +* Added the following to the list of "well-known" environment variables that are + automatically passed thru to runtimes: + + - `AUGUR_SEARCH_PATHS` + - `AUGUR_DEBUG` + - `AUGUR_PROFILE` + + ([#501](https://github.com/nextstrain/cli/pull/501)) (v10-4-2)= ## 10.4.2 (7 January 2026) diff --git a/doc/commands/build.rst b/doc/commands/build.rst index 566d78dd..7802d457 100644 --- a/doc/commands/build.rst +++ b/doc/commands/build.rst @@ -195,7 +195,7 @@ Options shared by all runtimes. .. option:: --env [=] - Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. + Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_SEARCH_PATHS``, ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AUGUR_DEBUG``, ``AUGUR_PROFILE``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. .. option:: --envdir diff --git a/doc/commands/run.rst b/doc/commands/run.rst index 7c4c59cc..09ea0fe5 100644 --- a/doc/commands/run.rst +++ b/doc/commands/run.rst @@ -197,7 +197,7 @@ Options shared by all runtimes. .. option:: --env [=] - Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. + Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_SEARCH_PATHS``, ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AUGUR_DEBUG``, ``AUGUR_PROFILE``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. .. option:: --envdir diff --git a/doc/commands/shell.rst b/doc/commands/shell.rst index e522229b..61b9f3f0 100644 --- a/doc/commands/shell.rst +++ b/doc/commands/shell.rst @@ -70,7 +70,7 @@ Options shared by all runtimes. .. option:: --env [=] - Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. + Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_SEARCH_PATHS``, ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AUGUR_DEBUG``, ``AUGUR_PROFILE``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. .. option:: --envdir diff --git a/doc/commands/view.rst b/doc/commands/view.rst index cd089bec..c407d1e0 100644 --- a/doc/commands/view.rst +++ b/doc/commands/view.rst @@ -132,7 +132,7 @@ Options shared by all runtimes. .. option:: --env [=] - Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. + Set the environment variable ```` to the value in the current environment (i.e. pass it thru) or to the given ````. May be specified more than once. Overrides any variables of the same name set via :option:`--envdir`. When this option or :option:`--envdir` is given, the default behaviour of automatically passing thru several "well-known" variables is disabled. The "well-known" variables are ``AUGUR_SEARCH_PATHS``, ``AUGUR_RECURSION_LIMIT``, ``AUGUR_MINIFY_JSON``, ``AUGUR_DEBUG``, ``AUGUR_PROFILE``, ``AWS_ACCESS_KEY_ID``, ``AWS_SECRET_ACCESS_KEY``, ``AWS_SESSION_TOKEN``, ``ID3C_URL``, ``ID3C_USERNAME``, ``ID3C_PASSWORD``, ``RETHINK_HOST``, and ``RETHINK_AUTH_KEY``. Pass those variables explicitly via :option:`--env` or :option:`--envdir` if you need them in combination with other variables. .. option:: --envdir diff --git a/nextstrain/cli/hostenv.py b/nextstrain/cli/hostenv.py index 419a7b3d..02d61159 100644 --- a/nextstrain/cli/hostenv.py +++ b/nextstrain/cli/hostenv.py @@ -16,9 +16,12 @@ # -trs, 13 Dec 2019 forwarded_names = [ - # Augur + # Augur + "AUGUR_SEARCH_PATHS", "AUGUR_RECURSION_LIMIT", "AUGUR_MINIFY_JSON", + "AUGUR_DEBUG", + "AUGUR_PROFILE", # AWS "AWS_ACCESS_KEY_ID",