From 960decbccdf91546c8c213f9fafcff23a74f3c13 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Fri, 15 Sep 2023 16:08:04 -0700
Subject: [PATCH] runner.conda: Explicitly install the latest package version
 during setup
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This our intent and expectation, and it's good to be explicit about it.
It may surface more installation issues, such as the one we observed in
monkeypox CI¹ with the latest version not being installable, but
obscuring those or surfacing them later on is _probably_ worse than
addressing them head on earlier.  This change will mean that any macOS
10.14 users, if any, would have to use

    NEXTSTRAIN_CONDA_BASE_PACKAGE="nextstrain-base ==20230615T171309Z"

since newer versions aren't installable for them.²

This behaviour also parallels update's behaviour since "runner.conda:
Explicitly specify a nextstrain-base version when updating" (d6e4f2b).
It was an oversight (on my part) to not use the same behaviour during
setup, but at the time I was focused on fixing an update bug.

Related-to: <https://github.com/nextstrain/conda-base/issues/41>
Related-to: <https://github.com/nextstrain/conda-base/pull/42>

¹ <https://github.com/nextstrain/monkeypox/issues/177>
² <https://github.com/nextstrain/conda-base/issues/38>
---
 nextstrain/cli/runner/conda.py | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/nextstrain/cli/runner/conda.py b/nextstrain/cli/runner/conda.py
index 3bd0a635..1cd0840c 100644
--- a/nextstrain/cli/runner/conda.py
+++ b/nextstrain/cli/runner/conda.py
@@ -247,23 +247,30 @@ def setup_prefix(dry_run: bool = False, force: bool = False) -> bool:
         if not dry_run:
             shutil.rmtree(str(PREFIX))
 
-    # Conda packages to install.
+    # We accept a package match spec, which one to three space-separated parts.¹
+    # If we got a spec, then we use it as-is.
+    #
+    # ¹ <https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/pkg-specs.html#package-match-specifications>
     #
-    # HEY YOU: If you add/remove packages here, make sure to account for how
-    # update() should make the same changes to existing envs.
-    #   -trs, 1 Sept 2022
-    packages = (
-        NEXTSTRAIN_BASE,
-    )
+    if " " in NEXTSTRAIN_BASE.strip():
+        install_spec = NEXTSTRAIN_BASE
+    else:
+        latest_version = (package_distribution(NEXTSTRAIN_CHANNEL, NEXTSTRAIN_BASE) or {}).get("version")
+
+        if latest_version:
+            install_spec = f"{NEXTSTRAIN_BASE} =={latest_version}"
+        else:
+            warn(f"Unable to find latest version of {NEXTSTRAIN_BASE} package; falling back to non-specific install")
+
+            install_spec = NEXTSTRAIN_BASE
 
     # Create environment
     print(f"Installing Conda packages into {PREFIX}…")
-    for pkg in packages:
-        print(f"  - {pkg}")
+    print(f"  - {install_spec}")
 
     if not dry_run:
         try:
-            micromamba("create", *packages)
+            micromamba("create", install_spec)
         except InternalError as err:
             warn(err)
             traceback.print_exc()