snakemake-executor-plugin-aws-batch-flex 0.1.0__tar.gz → 0.1.1__tar.gz

snakemake_executor_plugin_aws_batch_flex-0.1.1/.release-please-manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "0.1.1"
+}

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [0.1.1](https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex/compare/v0.1.0...v0.1.1) (2026-10-29)
+
+
+### Bug Fixes
+
+* big runs read peak memory from jobs across the whole run, not only the last ones ([147a054](https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex/commit/147a054053c7e7dbfee38029c95d9fa92dd44f00))
+* cancelling a run stops every job, also those Snakemake is checking on ([9edb388](https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex/commit/9edb3880575bb8d3c4fb2aceb469f7a120bfb3a4))
+* non-root images without curl get uv from their own conda at job start ([374cc30](https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex/commit/374cc303e6d1d42b17255dc36fe05c76ec84beff))
+* smkflex push gives the .gitignore note only when it uploaded, and no rate for tiny transfers ([6be28ad](https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex/commit/6be28ad2efe30a30f13c4c9bd077969f573024fb))
+
 ## 0.1.0 (2026-10-28)
 
 First release. Needs Snakemake 9 (9.5 or newer) and Python 3.11 to 3.13. Tested on Linux; macOS

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: snakemake-executor-plugin-aws-batch-flex
-Version: 0.1.0
+Version: 0.1.1
 Summary: Snakemake executor plugin for AWS Batch that runs every rule in its own container image
 Project-URL: Homepage, https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex
 Project-URL: Documentation, https://github.com/SSmith-NUIG/snakemake-executor-plugin-aws-batch-flex#getting-started

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/docs/reference.md

@@ -51,7 +51,7 @@ from the machine image (`host`); otherwise it's installed when each job starts,
 | `host-env-wait-seconds` | `120` | How long a job waits for that Snakemake if its machine is still setting it up when the job starts. A machine image made by `setup.sh` has it from the start, so 0 is fine there. |
 | `extra-packages` | *none* | Extra pip packages to install along with Snakemake when a job starts (e.g. `[pandas]`, or other Snakemake plugins). |
 | `python-version` | *the one you run Snakemake with* | The Python version to install Snakemake with when a job starts. |
-| `install-prereqs` | `false` | When installing at start: first install `curl` into images that have none of `curl`, `wget` or `pip`. |
+| `install-prereqs` | `false` | When installing at start, for images that have none of `curl`, `wget` or `pip`: get uv with the image's conda, mamba or micromamba (any user), or else install `curl` with its package manager (images that run as root). |
 | `script-python` | `image` | Which Python runs Python `script:` rules. `image`: the image's own, if it's 3.10 or newer, so the script can use the image's packages. `host`: always Snakemake's own. |
 
 **Memory, disk and Spot**

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/docs/setup.md

@@ -149,8 +149,9 @@ lines like `executor: aws-batch-flex` and `aws-batch-flex-queue: smkflex-queue`.
 To try the plugin on an existing Batch queue without building an AMI, set
 `aws-batch-flex-bootstrap: auto` in the profile instead of `host`. Snakemake is then installed into
 each container when its job starts (about 10-15 s per job), which needs internet access and
-`curl`, `wget` or `pip` in the image (`--aws-batch-flex-install-prereqs` installs `curl` first if
-missing).
+`curl`, `wget` or `pip` in the image. Without them, `--aws-batch-flex-install-prereqs` gets uv
+with the image's own conda, mamba or micromamba if it has one (as any user), or else installs
+`curl` with its package manager, which needs an image that runs as root.
 
 Or install the Snakemake env on each instance as it boots, with the stock ECS image and no AMI of
 your own: every new instance then spends about a minute on it before its first job (not yet

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "snakemake-executor-plugin-aws-batch-flex"
-version = "0.1.0"
+version = "0.1.1"
 description = "Snakemake executor plugin for AWS Batch that runs every rule in its own container image"
 dynamic = ["readme"]
 requires-python = ">=3.11"

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/src/snakemake_executor_plugin_aws_batch_flex/bootstrap.py

@@ -70,20 +70,29 @@ else
 fi"""
 
 
-# Installs curl (for uv) in an image without curl, wget or pip: only with install_prereqs
+# For an image without curl, wget or pip (only with install_prereqs): uv from the image's own
+# conda, mamba or micromamba into $SMK_BOOT, which works as any user and leaves the image's
+# environments alone; else curl from its package manager, which needs root
 _PREREQS = r'''
   if ! command -v curl >/dev/null 2>&1 && ! command -v wget >/dev/null 2>&1 \
      && ! { command -v python3 >/dev/null 2>&1 && python3 -m pip --version >/dev/null 2>&1; }; then
-    echo "[snakemake-batch] no curl/wget/pip in the image: installing curl, ca-certificates and bash" >&2
-    if [ "$(id -u)" != 0 ]; then
-      echo "[snakemake-batch] cannot install prerequisites: the image runs as a non-root user" >&2
-    elif command -v apt-get >/dev/null 2>&1; then
-      apt-get update -qq >&2 && DEBIAN_FRONTEND=noninteractive apt-get install -y -qq --no-install-recommends curl ca-certificates bash >&2 || true
-    elif command -v apk >/dev/null 2>&1; then apk add -q --no-cache curl ca-certificates bash >&2 || true
-    elif command -v dnf >/dev/null 2>&1; then dnf install -y -q curl ca-certificates bash >&2 || true
-    elif command -v microdnf >/dev/null 2>&1; then microdnf install -y curl ca-certificates bash >&2 || true
-    elif command -v yum >/dev/null 2>&1; then yum install -y -q curl ca-certificates bash >&2 || true
-    else echo "[snakemake-batch] no known package manager in the image" >&2
+    SMK_CONDA=$(command -v micromamba || command -v mamba || command -v conda || true)
+    if [ -n "$SMK_CONDA" ]; then
+      echo "[snakemake-batch] no curl/wget/pip in the image: getting uv with its $SMK_CONDA" >&2
+      CONDA_PKGS_DIRS="$SMK_BOOT/pkgs" "$SMK_CONDA" create -y -q -p "$SMK_BOOT/uvenv" -c conda-forge "uv=@@UVVER@@" >&2 \
+        && mkdir -p "$SMK_BOOT/bin" && ln -sf "$SMK_BOOT/uvenv/bin/uv" "$SMK_BOOT/bin/uv" || true
+    elif [ "$(id -u)" != 0 ]; then
+      echo "[snakemake-batch] no curl/wget/pip/conda in the image, and it runs as a non-root user, so none can be installed. Add curl to the image (or USER root), or run the rule on EC2 (batch_queue), where Snakemake comes from the AMI" >&2
+    else
+      echo "[snakemake-batch] no curl/wget/pip in the image: installing curl, ca-certificates and bash" >&2
+      if command -v apt-get >/dev/null 2>&1; then
+        apt-get update -qq >&2 && DEBIAN_FRONTEND=noninteractive apt-get install -y -qq --no-install-recommends curl ca-certificates bash >&2 || true
+      elif command -v apk >/dev/null 2>&1; then apk add -q --no-cache curl ca-certificates bash >&2 || true
+      elif command -v dnf >/dev/null 2>&1; then dnf install -y -q curl ca-certificates bash >&2 || true
+      elif command -v microdnf >/dev/null 2>&1; then microdnf install -y curl ca-certificates bash >&2 || true
+      elif command -v yum >/dev/null 2>&1; then yum install -y -q curl ca-certificates bash >&2 || true
+      else echo "[snakemake-batch] no known package manager in the image" >&2
+      fi
     fi
   fi
 '''
@@ -277,7 +286,7 @@ def build_prelude(
         _TEMPLATE.replace("@@WORKDIR@@", WORKDIR)
         .replace("@@CHECK@@", check)
         .replace("@@PYVER@@", shlex.quote(python_version))
-        .replace("@@PREREQS@@", _PREREQS if install_prereqs else "")
+        .replace("@@PREREQS@@", _PREREQS.replace("@@UVVER@@", UV_VERSION) if install_prereqs else "")
         .replace("@@REQS@@", reqs)
         .replace("@@NEWER@@", f"--exclude-newer {shlex.quote(resolved_at)} " if resolved_at else "")
         .replace("@@UV@@", uv_snippet("$SMK_BOOT/bin", "$SMK_BOOT/uvlib"))

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/src/snakemake_executor_plugin_aws_batch_flex/executor.py

@@ -156,6 +156,9 @@ class Executor(RemoteExecutor):
         self._warned_fargate_shm = False
         self._said_resolved = False
         self._warned_tags: set = set()
+        # Batch jobs submitted and not seen to end. Cancelling stops these too: while Snakemake
+        # checks on its running jobs, it takes them out of the list it would hand cancel_jobs.
+        self._unfinished: set = set()
         self._warned_disk: set = set()
         self._existing_defs: dict = {}  # ref -> ExistingJobDefinition
         self._fair_share: dict = {}  # queue -> has a scheduling policy
@@ -578,6 +581,7 @@ class Executor(RemoteExecutor):
             f"Submitted {job.name} as AWS Batch job {resp['jobId']} "
             f"({image}, {req.vcpu} vCPU, {req.memory_mib} MiB, queue {queue}, {platform})"
         )
+        self._unfinished.add(resp["jobId"])
         self.report_job_submission(
             SubmittedJobInfo(
                 job,
@@ -608,6 +612,8 @@ class Executor(RemoteExecutor):
 
         for jid, info in by_id.items():
             d = described.get(jid)
+            if d is None or d["status"] in ("SUCCEEDED", "FAILED"):
+                self._unfinished.discard(jid)
             if d is None:
                 self.report_job_error(
                     info, msg=f"AWS Batch no longer knows job {jid} (expired?)."
@@ -658,16 +664,16 @@ class Executor(RemoteExecutor):
     def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
         # In parallel: a head job that is stopped has little time (ECS_CONTAINER_STOP_TIMEOUT)
         # to cancel every job and save its state.
-        def cancel(info):
+        def cancel(jid):
             try:
-                self.batch.terminate_job(
-                    jobId=info.external_jobid, reason="Cancelled by Snakemake"
-                )
+                self.batch.terminate_job(jobId=jid, reason="Cancelled by Snakemake")
             except (ClientError, BotoCoreError) as e:
-                self.logger.warning(f"Could not terminate {info.external_jobid}: {e}")
+                self.logger.warning(f"Could not terminate {jid}: {e}")
 
+        # set() copies at once, so the status checks can't change it meanwhile
+        ids = {i.external_jobid for i in active_jobs} | set(self._unfinished)
         with ThreadPoolExecutor(CANCEL_THREADS) as pool:
-            list(pool.map(cancel, active_jobs))
+            list(pool.map(cancel, sorted(ids)))
 
     def _warn_if_stuck(self, d: dict, info: SubmittedJobInfo):
         sub = _sub(info)

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/src/snakemake_executor_plugin_aws_batch_flex/transfer.py

@@ -78,8 +78,11 @@ def _transfer(jobs, work, verb):
     return done, total, secs
 
 def _rate(total, secs):
-    mb = total / 1e6
-    return f"{mb:.1f} MB in {secs:.0f} s ({mb / secs:.1f} MB/s)" if total else ""
+    """How much was sent, and how fast when that means something (1 MB or more, over a second)."""
+    if not total:
+        return ""
+    size = f"{total / 1e6:.1f} MB" if total >= 1e5 else f"{total / 1e3:.1f} kB" if total >= 1e3 else f"{total} bytes"
+    return f"{size} in {secs:.0f} s ({total / 1e6 / secs:.1f} MB/s)" if total >= 1e6 and secs >= 1 else size
 
 def cmd_pull(a):
     _dir, profile = _load_profile(a.profile)
@@ -176,7 +179,8 @@ def cmd_push(a):
         rate = _rate(total, secs)
         print(f"{sent} uploaded to {prefix}" + (f" ({rate})" if rate else "")
               + (f", {skipped} already there (unchanged; --force sends them again)" if skipped else ""))
-        _hint_gitignore([p for p in a.paths if not os.path.isabs(p)])
+        if sent:  # not again on every push that had nothing new
+            _hint_gitignore([p for p in a.paths if not os.path.isabs(p)])
     return 0
 
 def _hint_gitignore(paths):

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/src/snakemake_executor_plugin_aws_batch_flex/usage.py

@@ -83,8 +83,10 @@ class Usage:
         todo = []
         for rule, streams in self.logs.items():
             if total > ALL_PEAKS and len(streams) > PEAK_SAMPLE:
+                # spread over the run: a rule's biggest inputs aren't always its last jobs
                 self.sampled = True
-                streams = streams[-PEAK_SAMPLE:]
+                step = len(streams) / PEAK_SAMPLE
+                streams = [streams[int(i * step)] for i in range(PEAK_SAMPLE)]
             todo += [(rule, g, st) for g, st in streams]
 
         def one(item):

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/tests/test_integration.py

@@ -469,8 +469,8 @@ def test_workdir_directive_stops_before_submitting(tmp_path):
 
 
 def test_job_commands_fit_what_ecs_allows(tmp_path):
-    # installing Snakemake at job start makes the longest commands
-    r, calls = run(tmp_path, SNAKEFILE, "--aws-batch-flex-bootstrap", "always")
+    # installing Snakemake at job start, with the prerequisites, makes the longest commands
+    r, calls = run(tmp_path, SNAKEFILE, "--aws-batch-flex-bootstrap", "always", "--aws-batch-flex-install-prereqs")
     assert r.returncode == 0, r.stdout + r.stderr
     sizes = [c["overrides_chars"] for c in calls if c["call"] == "submit_job"]
     assert sizes and max(sizes) < 8192 - 500, sizes  # room for a longer storage prefix and the like

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/tests/test_prereqs.py

@@ -1,4 +1,4 @@
-"""The curl/ca-certificates fallback, run in a stripped PATH with stub package managers."""
+"""The fallbacks for images without curl, wget or pip, run in a stripped PATH with stub tools."""
 import os, stat, subprocess
 from snakemake_executor_plugin_aws_batch_flex.bootstrap import build_prelude
 
@@ -42,7 +42,13 @@ def test_off_by_default_installs_nothing_and_fails_clearly(tmp_path):
 
 def test_non_root_is_reported_not_attempted(tmp_path):
     r, calls = _run(tmp_path, True, ["apt-get"], uid="1000")
-    assert calls == "" and "non-root" in r.stderr
+    assert calls == "" and "non-root" in r.stderr and "batch_queue" in r.stderr
+
+
+def test_uv_from_the_images_conda_as_any_user(tmp_path):
+    # mambaorg/micromamba: non-root, no curl; its micromamba fetches uv into the job's folder
+    r, calls = _run(tmp_path, True, ["apt-get", "micromamba"], uid="1000")
+    assert "micromamba create -y -q -p" in calls and "-c conda-forge uv=" in calls and "apt-get" not in calls
 
 
 def test_skipped_when_curl_already_present(tmp_path):

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/tests/test_smkflex.py

@@ -336,6 +336,13 @@ def test_push(tmp_path):
     assert (tmp_path / "store" / "data" / "a.fq").read_text() == "CCC"
     r, _ = smkflex(wf, "push", "../x")
     assert r.returncode == 2 and "outside the workflow folder" in r.stderr
+    # a folder smkflex run would send too: said once, not on every push with nothing new
+    (wf / "refs").mkdir()
+    (wf / "refs" / "g.fa").write_text(">g\n")
+    r, _ = smkflex(wf, "push", "refs")
+    assert "add to .gitignore:\nrefs/" in r.stdout and "uploaded to" in r.stdout and "MB/s" not in r.stdout
+    r, _ = smkflex(wf, "push", "refs")
+    assert "0 uploaded" in r.stdout and ".gitignore" not in r.stdout
 
 
 def test_push_absolute_paths_and_many_files(tmp_path):

{snakemake_executor_plugin_aws_batch_flex-0.1.0 → snakemake_executor_plugin_aws_batch_flex-0.1.1}/tests/test_units.py

@@ -221,6 +221,7 @@ def test_sources_patch_leaves_other_executors_alone(tmp_path, monkeypatch):
 
 
 def test_cancel_terminates_jobs_in_parallel_and_goes_on_after_errors():
+    # also j20, which Snakemake leaves out of the list while it checks on it
     import threading, time, types
     from botocore.exceptions import ClientError
     from snakemake_executor_plugin_aws_batch_flex.executor import Executor
@@ -235,12 +236,12 @@ def test_cancel_terminates_jobs_in_parallel_and_goes_on_after_errors():
             done.append(jobId)
 
     me = types.SimpleNamespace(batch=types.SimpleNamespace(terminate_job=terminate_job),
-                               logger=types.SimpleNamespace(warning=warnings.append))
+                               logger=types.SimpleNamespace(warning=warnings.append), _unfinished={"j1", "j20"})
     jobs = [types.SimpleNamespace(external_jobid=f"j{i}") for i in range(20)]
     start = time.time()
     Executor.cancel_jobs(me, jobs)
     assert time.time() - start < 2  # one at a time would take 4 s
-    assert sorted(done) == sorted(f"j{i}" for i in range(20) if i != 3)
+    assert sorted(done) == sorted(f"j{i}" for i in range(21) if i != 3)  # j1 once
     assert len(warnings) == 1 and "j3" in warnings[0]
 
 
@@ -316,6 +317,24 @@ def test_rules_whose_jobs_ran_out_get_no_memory_suggestion(tmp_path, monkeypatch
     assert "Hint: in killed's jobs, Linux killed 2 process(es) for lack of memory" in u.table(256)
 
 
+def test_big_runs_sample_jobs_from_the_whole_run():
+    from snakemake_executor_plugin_aws_batch_flex import usage
+    u = usage.Usage()
+    for i in range(usage.ALL_PEAKS + 100):  # the first jobs took the most memory
+        u.add("align", {"startedAt": 0, "stoppedAt": 1000}, 1, 4352, "ec2")
+        u.add_log("align", "g", str(i))
+    client = types.SimpleNamespace(get_log_events=lambda logGroupName, logStreamName, **kw: {
+        "events": [{"message": f"[snakemake-batch] peak-memory-bytes={(4000 - int(logStreamName)) << 20}"}]})
+    u.fetch_peaks(client)
+    assert len(u.peaks["align"]) == usage.PEAK_SAMPLE and max(u.peaks["align"]) == 4000
+
+
+def test_transfer_sizes():
+    from snakemake_executor_plugin_aws_batch_flex.transfer import _rate
+    assert (_rate(0, 1), _rate(12, 0.01), _rate(4300, 0.01)) == ("", "12 bytes", "4.3 kB")
+    assert _rate(250_000_000, 10) == "250.0 MB in 10 s (25.0 MB/s)"
+
+
 def test_hint_for_a_script_that_wasnt_sent():
     from snakemake_executor_plugin_aws_batch_flex.hints import known_problem_hints as hints
     py = ["python: can't open file '/tmp/snakemake-job-7/scripts/synthetic/gen.py': [Errno 2] No such file or directory"]

snakemake_executor_plugin_aws_batch_flex-0.1.0/.release-please-manifest.json

@@ -1,3 +0,0 @@
-{
-  ".": "0.1.0"
-}