Skip to content

Sync Augur env var list #501

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
victorlin merged 1 commit into from
Jan 30, 2026
Merged

Sync Augur env var list #501

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 10 additions & 0 deletions CHANGES.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
11 changes: 11 additions & 0 deletions doc/changes.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion doc/commands/build.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ Options shared by all runtimes.

.. option:: --env <name>[=<value>]

Set the environment variable ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 <path>

Expand Down
2 changes: 1 addition & 1 deletion doc/commands/run.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ Options shared by all runtimes.

.. option:: --env <name>[=<value>]

Set the environment variable ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 <path>

Expand Down
2 changes: 1 addition & 1 deletion doc/commands/shell.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ Options shared by all runtimes.

.. option:: --env <name>[=<value>]

Set the environment variable ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 <path>

Expand Down
2 changes: 1 addition & 1 deletion doc/commands/view.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ Options shared by all runtimes.

.. option:: --env <name>[=<value>]

Set the environment variable ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 ``<name>`` to the value in the current environment (i.e. pass it thru) or to the given ``<value>``. 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 <path>

Expand Down
5 changes: 4 additions & 1 deletion nextstrain/cli/hostenv.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,12 @@
# -trs, 13 Dec 2019

forwarded_names = [
# Augur <https://nextstrain-augur.readthedocs.io/en/stable/envvars.html>
# Augur <https://docs.nextstrain.org/projects/augur/en/stable/usage/envvars.html>
"AUGUR_SEARCH_PATHS",
"AUGUR_RECURSION_LIMIT",
"AUGUR_MINIFY_JSON",
"AUGUR_DEBUG",
"AUGUR_PROFILE",

# AWS
"AWS_ACCESS_KEY_ID",
Expand Down
Loading