Ac tests

.github/workflows/cgatcore_python.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -43,5 +43,5 @@ jobs:
           conda list
       - name: Test
         run: |
-          python setup.py install
+          pip install .
           ./all-tests.sh

all-tests.sh

@@ -1,13 +1,18 @@
-#! /bin/bash
+#!/bin/bash
 
 set -xue
 
+# Run code style checks
 pycodestyle
+
+# Run the template pipeline script with the `make all` command
 python tests/template_pipeline.py make all
-nosetests -v tests/test_import.py
-nosetests -v tests/test_iotools.py
-nosetests -v tests/test_pipeline_cluster.py
-nosetests -v tests/test_pipeline_control.py
-nosetests -v tests/test_pipeline_execution.py
-pytest tests/test_pipeline_cli.py
-pytest tests/test_pipeline_actions.py
+
+# Run tests using pytest
+pytest -v tests/test_import.py
+pytest -v tests/test_iotools.py
+pytest -v tests/test_pipeline_cluster.py
+pytest -v tests/test_pipeline_control.py
+pytest -v tests/test_pipeline_execution.py
+pytest -v tests/test_pipeline_cli.py
+pytest -v tests/test_pipeline_actions.py

cgatcore/csvutils.py

@@ -221,7 +221,7 @@ def readTable(infile,
                     raise ValueError(
                         "missing elements in line %s, received=%s, "
                         "expected=%s" %
-                        (r, str(row),  str(fields)))
+                        (r, str(row), str(fields)))
 
                 raise ValueError
 

cgatcore/iotools.py

@@ -609,7 +609,7 @@ def bytes2human(n, format='%(value).1f%(symbol)s', symbols='customary'):
     symbols = SYMBOLS[symbols]
     prefix = {}
     for i, s in enumerate(symbols[1:]):
-        prefix[s] = 1 << (i+1)*10
+        prefix[s] = 1 << (i + 1) * 10
     for symbol in reversed(symbols[1:]):
         if n >= prefix[symbol]:
             value = float(n) / prefix[symbol]
@@ -668,7 +668,7 @@ def human2bytes(s):
             raise ValueError("can't interpret %r" % init)
     prefix = {sset[0]: 1}
     for i, s in enumerate(sset[1:]):
-        prefix[s] = 1 << (i+1)*10
+        prefix[s] = 1 << (i + 1) * 10
 
     return int(num * prefix[letter])
 

cgatcore/logfile.py

@@ -35,8 +35,8 @@
 
 RuntimeInformation = collections.namedtuple(
     "RuntimeInformation",
-    "script options jobid host has_finished " +
-    "start_date end_date " +
+    "script options jobid host has_finished "
+    "start_date end_date "
     "wall utime stime cutime cstime")
 
 RX_START = re.compile(r"output generated by (\S+) (.*)")

cgatcore/pipeline/execution.py

@@ -1386,8 +1386,8 @@ def run_pickled(params):
     try:
         function = getattr(module, func_name)
     except AttributeError as msg:
-        raise AttributeError(msg.message +
-                             "unknown function, available functions are: %s" %
+        raise AttributeError(msg.message
+                             + "unknown function, available functions are: %s" %
                              ",".join([x for x in dir(module)
                                        if not x.startswith("_")]))
 

cgatcore/pipeline/farm.py

@@ -234,8 +234,7 @@ def chunk_iterator_regex_split(infile, args, prefix, use_header=False):
         if line[0] == "#":
             continue
         if rex.search(line[:-1]):
-            if n > 0 and (n % chunk_size == 0 or
-                          (max_lines and nlines > max_lines)):
+            if n > 0 and (n % chunk_size == 0 or (max_lines and nlines > max_lines)):
                 outfile.close()
                 yield filename
                 filename = "%s/%010i.in" % (prefix, n)

cgatcore/pipeline/logstash_formatter/__init__.py

@@ -171,8 +171,8 @@ def format(self, record):
         now = datetime.datetime.utcnow()
         event_time = getattr(record,
                              "eventtime",
-                             now.strftime("%Y-%m-%dT%H:%M:%S") +
-                             ".%03d" % (now.microsecond / 1000) + "Z")
+                             now.strftime("%Y-%m-%dT%H:%M:%S")
+                             + ".%03d" % (now.microsecond / 1000) + "Z")
         base_log = {'@timestamp': event_time,
                     '@version': 1,
                     'source_host': self.source_host}

cgatcore/pipeline/utils.py

@@ -109,8 +109,7 @@ def _doc(func):
             # currently hard-coded, can be derived
             # from doc string?
             if not replace:
-                lines.insert(x+1, " " * 4 +
-                             func.__doc__)
+                lines.insert(x + 1, " " * 4 + func.__doc__)
                 func.__doc__ = "\n".join(lines)
             else:
                 func.__doc__ = value.__doc__

cgatcore/remote/ftp.py

@@ -24,9 +24,9 @@ def __init__(self, *args, stay_on_remote=False, immediate_close=False, **kwargs)
     @contextmanager
     def ftpc(self):
 
-        if (not hasattr(self, "conn") or
-            (hasattr(self, "conn") and
-             not isinstance(self.conn, ftputil.FTPHost))) or self.immediate_close:
+        if (not hasattr(self, "conn")
+            or (hasattr(self, "conn") and not isinstance(self.conn, ftputil.FTPHost)))
+        or self.immediate_close:
             args_use = self.provider.args
             if len(self.args):
                 args_use = self.args