flake8 to ruff (#3495)

* flake8 to ruff

* . import

* check_analysis_access

Author: antgonza

.github/workflows/qiita-ci.yml

@@ -252,7 +252,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - name: flake8
+      - name: ruff
         uses: actions/setup-python@v2
         with:
           python-version: "3.9"
@@ -262,5 +262,5 @@ jobs:
         uses: actions/checkout@v2
       - name: lint
         run: |
-          pip install -q flake8
-          flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py
+          pip install -q ruff
+          ruff check qiita_* setup.py scripts/qiita* notebooks/*/*.py

notebooks/resource-allocation/generate-allocation-summary-arrays.py

@@ -1,35 +1,44 @@
-from subprocess import check_output
-import pandas as pd
 from datetime import datetime, timedelta
 from io import StringIO
 from json import loads
 from os.path import join
+from subprocess import check_output
+
+import pandas as pd
 
-from qiita_db.util import MaxRSS_helper
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.processing_job import ProcessingJob
 from qiita_db.software import Software
-
+from qiita_db.util import MaxRSS_helper
 
 all_commands = [c for s in Software.iter(False) for c in s.commands]
 
 # retrieving only the numerice external_id means that we are only focusing
 # on barnacle2/slurm jobs
-main_jobs = [j for c in all_commands for j in c.processing_jobs
-             if j.status == 'success' and j.external_id.isnumeric()]
-
-sacct = ['sacct', '-p', '--format=JobID,ElapsedRaw,MaxRSS,Submit,Start,MaxRSS,'
-         'CPUTimeRAW,ReqMem,AllocCPUs,AveVMSize', '-j']
+main_jobs = [
+    j
+    for c in all_commands
+    for j in c.processing_jobs
+    if j.status == "success" and j.external_id.isnumeric()
+]
+
+sacct = [
+    "sacct",
+    "-p",
+    "--format=JobID,ElapsedRaw,MaxRSS,Submit,Start,MaxRSS,"
+    "CPUTimeRAW,ReqMem,AllocCPUs,AveVMSize",
+    "-j",
+]
 
 data = []
 for i, j in enumerate(main_jobs):
     if i % 1000 == 0:
-        print(f'{i}/{len(main_jobs)}')
+        print(f"{i}/{len(main_jobs)}")
     eid = j.external_id
-    extra_info = ''
-    rvals = StringIO(check_output(sacct + [eid]).decode('ascii'))
-    _d = pd.read_csv(rvals, sep='|')
-    _d['QiitaID'] = j.id
+    extra_info = ""
+    rvals = StringIO(check_output(sacct + [eid]).decode("ascii"))
+    _d = pd.read_csv(rvals, sep="|")
+    _d["QiitaID"] = j.id
     cmd = j.command
     s = j.command.software
     try:
@@ -43,44 +52,49 @@
     except TypeError as e:
         # similar to the except above, exept that for these 2 commands, we have
         # the study_id as None
-        if cmd.name in {'create_sample_template', 'delete_sample_template',
-                        'list_remote_files'}:
+        if cmd.name in {
+            "create_sample_template",
+            "delete_sample_template",
+            "list_remote_files",
+        }:
             continue
         else:
             raise e
 
     sname = s.name
 
-    if cmd.name == 'release_validators':
-        ej = ProcessingJob(j.parameters.values['job'])
+    if cmd.name == "release_validators":
+        ej = ProcessingJob(j.parameters.values["job"])
         extra_info = ej.command.name
         samples, columns, input_size = ej.shape
-    elif cmd.name == 'complete_job':
-        artifacts = loads(j.parameters.values['payload'])['artifacts']
+    elif cmd.name == "complete_job":
+        artifacts = loads(j.parameters.values["payload"])["artifacts"]
         if artifacts is not None:
-            extra_info = ','.join({
-                x['artifact_type'] for x in artifacts.values()
-                if 'artifact_type' in x})
-    elif cmd.name == 'Validate':
-        input_size = sum([len(x) for x in loads(
-            j.parameters.values['files']).values()])
+            extra_info = ",".join(
+                {x["artifact_type"] for x in artifacts.values() if "artifact_type" in x}
+            )
+    elif cmd.name == "Validate":
+        input_size = sum([len(x) for x in loads(j.parameters.values["files"]).values()])
         sname = f"{sname} - {j.parameters.values['artifact_type']}"
-    elif cmd.name == 'Alpha rarefaction curves [alpha_rarefaction]':
+    elif cmd.name == "Alpha rarefaction curves [alpha_rarefaction]":
         extra_info = j.parameters.values[
-            ('The number of rarefaction depths to include between min_depth '
-             'and max_depth. (steps)')]
-
-    _d['external_id'] = eid
-    _d['sId'] = s.id
-    _d['sName'] = sname
-    _d['sVersion'] = s.version
-    _d['cId'] = cmd.id
-    _d['cName'] = cmd.name
-    _d['samples'] = samples
-    _d['columns'] = columns
-    _d['input_size'] = input_size
-    _d['extra_info'] = extra_info
-    _d.drop(columns=['Unnamed: 10'], inplace=True)
+            (
+                "The number of rarefaction depths to include between min_depth "
+                "and max_depth. (steps)"
+            )
+        ]
+
+    _d["external_id"] = eid
+    _d["sId"] = s.id
+    _d["sName"] = sname
+    _d["sVersion"] = s.version
+    _d["cId"] = cmd.id
+    _d["cName"] = cmd.name
+    _d["samples"] = samples
+    _d["columns"] = columns
+    _d["input_size"] = input_size
+    _d["extra_info"] = extra_info
+    _d.drop(columns=["Unnamed: 10"], inplace=True)
     data.append(_d)
 
 data = pd.concat(data)
@@ -100,34 +114,33 @@
 #                         external_id but separate from external_id.batch.
 # Here we are going to merge all this info into a single row + some
 # other columns
-date_fmt = '%Y-%m-%dT%H:%M:%S'
+date_fmt = "%Y-%m-%dT%H:%M:%S"
 
 df = []
-for eid, __df in data.groupby('external_id'):
+for eid, __df in data.groupby("external_id"):
     tmp = __df.iloc[1].copy()
     # Calculating WaitTime, basically how long did the job took to start
     # this is useful for some general profiling
-    tmp['WaitTime'] = datetime.strptime(
-        __df.iloc[0].Start, date_fmt) - datetime.strptime(
-        __df.iloc[0].Submit, date_fmt)
+    tmp["WaitTime"] = datetime.strptime(
+        __df.iloc[0].Start, date_fmt
+    ) - datetime.strptime(__df.iloc[0].Submit, date_fmt)
     df.append(tmp)
 df = pd.DataFrame(df)
 
 # This is important as we are transforming the MaxRSS to raw value
 # so we need to confirm that there is no other suffixes
-print('Make sure that only 0/K/M exist', set(
-    df.MaxRSS.apply(lambda x: str(x)[-1])))
+print("Make sure that only 0/K/M exist", set(df.MaxRSS.apply(lambda x: str(x)[-1])))
 
 # Generating new columns
-df['MaxRSSRaw'] = df.MaxRSS.apply(lambda x: MaxRSS_helper(str(x)))
-df['ElapsedRawTime'] = df.ElapsedRaw.apply(
-    lambda x: timedelta(seconds=float(x)))
+df["MaxRSSRaw"] = df.MaxRSS.apply(lambda x: MaxRSS_helper(str(x)))
+df["ElapsedRawTime"] = df.ElapsedRaw.apply(lambda x: timedelta(seconds=float(x)))
 
 # Thu, Apr 27, 2023 was the first time Jeff and I changed the old allocations
 # (from barnacle) to a better allocation so using job 1265533 as the
 # before/after so we only use the latests for the newest version
-df['updated'] = df.external_id.apply(
-    lambda x: 'after' if int(x) >= 1265533 else 'before')
+df["updated"] = df.external_id.apply(
+    lambda x: "after" if int(x) >= 1265533 else "before"
+)
 
-fn = join('/panfs', 'qiita', f'jobs_{df.Start.max()[:10]}.tsv.gz')
-df.to_csv(fn, sep='\t', index=False)
+fn = join("/panfs", "qiita", f"jobs_{df.Start.max()[:10]}.tsv.gz")
+df.to_csv(fn, sep="\t", index=False)