Revert "Merge pull request #124 from magnusuMET/linting"

This reverts commit 5afa6a3, reversing changes made to 3ac043d.
metno · Aug 3, 2023 · 61de1a3 · 61de1a3
1 parent 5afa6a3
commit 61de1a3
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Showing 49 changed files with 2,078 additions and 2,807 deletions.
diff --git a/install_usermodule_r8.sh b/install_usermodule_r8.sh
@@ -116,9 +116,12 @@ EOF
 install_snap() {
     MODULE_VERSION="$1"
     BASE_MODULE_VERSION="$2"
+
+    source /modules/rhel8/conda/install/etc/profile.d/conda.sh
+
     BASE_MODULE_PREFIX=/modules/rhel8/user-apps/fou-modules/SnapPy/"$BASE_MODULE_VERSION"/
 
-    source /modules/rhel8/conda/install/etc/profile.d/conda.sh "$BASE_MODULE_PREFIX"
+    conda activate "$BASE_MODULE_PREFIX"
 
     MODULE_PREFIX=/modules/rhel8/user-apps/fou-modules/SnapPy/"$MODULE_VERSION"/
     mkdir --parent -- "$MODULE_PREFIX/bin"

diff --git a/utils/SnapPy/METNO/Alvin.py b/utils/SnapPy/METNO/Alvin.py
@@ -1,25 +1,25 @@
 # SNAP: Servere Nuclear Accident Programme
 # Copyright (C) 1992-2017   Norwegian Meteorological Institute
-#
-# This file is part of SNAP. SNAP is free software: you can
-# redistribute it and/or modify it under the terms of the
-# GNU General Public License as published by the
+# 
+# This file is part of SNAP. SNAP is free software: you can 
+# redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the 
 # Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-#
+# 
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-#
+# 
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-"""
+'''
 Created on Apr 28, 2017
 
 @author: heikok
-"""
+'''
 import os
 from subprocess import TimeoutExpired
 from time import sleep
@@ -31,24 +31,22 @@
 
 
 class Alvin(HPC):
-    """
+    '''
     Implementation of a HPC machine for alvin.nsc.liu.se
-    """
+    '''
+
 
     def __init__(self):
-        """
+        '''
         Constructor
-        """
-        connection = SSHConnection(
-            username="metno_op", machine="alvin.nsc.liu.se", port=22
-        )
+        '''
+        connection = SSHConnection(username="metno_op", machine="alvin.nsc.liu.se", port=22)
         queue = SLURMQueue()
         super().__init__(connection, queue)
 
 
 class TestFrost(unittest.TestCase):
-    """tests for alvin, only working when having an existing forecast account on alvin"""
-
+    '''tests for alvin, only working when having an existing forecast account on alvin'''
     def setUp(self):
         unittest.TestCase.setUp(self)
         self.hpc = HPC.by_name("alvin")
@@ -58,14 +56,15 @@ def setUp(self):
     def tearDown(self):
         unittest.TestCase.tearDown(self)
         for f in self.testFiles:
-            if os.path.exists(f):
+            if (os.path.exists(f)):
                 os.unlink(f)
 
     def test_connect(self):
         (out, error, retval) = self.hpc.syscall("echo", ["5"])
         self.assertEqual(retval, 0, "command succeeded")
         self.assertEqual(int(out), 5, "command output correct")
 
+
     def test_timeout(self):
         with self.assertRaises(TimeoutExpired):
             self.hpc.syscall("sleep", ["5"], timeout=1)
@@ -75,8 +74,7 @@ def test_full(self):
         self.hpc.syscall("rm", ["-r", self.rdir])
         self.hpc.syscall("mkdir", ["-p", self.rdir])
         with open(self.testFiles[0], "w") as fh:
-            fh.write(
-                """#! /bin/bash
+            fh.write('''#! /bin/bash
 
 #SBATCH -A met
 #SBATCH --nodes=1 --ntasks-per-node=1 --time=01:00:00
@@ -86,10 +84,7 @@ def test_full(self):
 
 sleep 8
 echo "finished" > {status}
-            """.format(
-                    status=status_file, rdir=self.rdir
-                )
-            )
+            '''.format(status=status_file, rdir=self.rdir))
         self.hpc.put_files([self.testFiles[0]], self.rdir)
         qjob = self.hpc.submit_job(os.path.join(self.rdir, self.testFiles[0]), [])
         self.assertIsNotNone(qjob, "job submitted")
@@ -114,6 +109,5 @@ def test_full(self):
 
         self.hpc.syscall("rm", ["-r", self.rdir])
 
-
 if __name__ == "__main__":
     unittest.main()
diff --git a/utils/SnapPy/METNO/DirectConnection.py b/utils/SnapPy/METNO/DirectConnection.py
@@ -1,25 +1,25 @@
 # SNAP: Servere Nuclear Accident Programme
 # Copyright (C) 1992-2017   Norwegian Meteorological Institute
-#
-# This file is part of SNAP. SNAP is free software: you can
-# redistribute it and/or modify it under the terms of the
-# GNU General Public License as published by the
+# 
+# This file is part of SNAP. SNAP is free software: you can 
+# redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the 
 # Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-#
+# 
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-#
+# 
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-"""
+'''
 Created on Aug 08, 2017
 
 @author: heikok
-"""
+'''
 
 import os
 import shutil
@@ -31,10 +31,11 @@
 
 
 class DirectConnection(Connection):
-    """no connection, working directly on that machine"""
+    '''no connection, working directly on that machine
 
+    '''
     charset = typed_property("charset", str)
-    """charset of stdout of the machine, usually utf-8"""
+    '''charset of stdout of the machine, usually utf-8'''
 
     def __init__(self):
         super().__init__()
@@ -55,28 +56,25 @@ def get_files(self, files, local_path=None, timeout=None):
 
     def syscall(self, program, args, timeout=None):
         if sys.version_info > (3, 5, 0):
-            proc = subprocess.run(
-                [program] + args,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.PIPE,
-                timeout=timeout,
-            )
-            return (
-                proc.stdout.decode(self.charset),
-                proc.stderr.decode(self.charset),
-                proc.returncode,
-            )
+            proc = subprocess.run([program]+ args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, timeout=timeout)
+            return (proc.stdout.decode(self.charset),
+                    proc.stderr.decode(self.charset),
+                    proc.returncode)
         else:
             try:
                 output = subprocess.check_output([program] + args, timeout=timeout)
-                return (output.decode(self.charset), "", 0)
+                return (output.decode(self.charset),
+                        '',
+                        0)
             except subprocess.CalledProcessError as cpe:
-                return (cpe.output.decode(self.charset), "", cpe.returncode)
+                return (cpe.output.decode(self.charset),
+                        '',
+                        cpe.returncode)
 
 
-class TestDirectConnection(unittest.TestCase):
-    """Test for DirectConnection"""
 
+class TestDirectConnection(unittest.TestCase):
+    '''Test for DirectConnection'''
     def setUp(self):
         unittest.TestCase.setUp(self)
         self.dir1 = os.path.join(os.path.dirname(__file__), "testdir1")
@@ -86,17 +84,19 @@ def setUp(self):
         if not os.path.exists(self.dir2):
             os.mkdir(self.dir2)
 
-        self.files = ["file1", "file2"]
+        self.files = ['file1', 'file2']
         for file in self.files:
             infile = os.path.join(self.dir1, file)
             if not os.path.exists(infile):
-                with open(infile, "w") as ifh:
+                with open(infile, 'w') as ifh:
                     ifh.write("file: {name}".format(name=infile))
             outfile = os.path.join(self.dir2, file)
             if os.path.exists(outfile):
                 os.unlink(outfile)
         self.conn = DirectConnection()
 
+
+
     def tearDown(self):
         unittest.TestCase.tearDown(self)
         for path in (self.dir1, self.dir2):
@@ -120,7 +120,8 @@ def test_get_files(self):
         files_o = [os.path.join(self.dir2, x) for x in self.files]
         self.conn.get_files(files_i, self.dir2, 5)
         for file in files_o:
-            self.assertTrue(os.path.exists(file), "file {} exists".format(file))
+            self.assertTrue(os.path.exists(file),
+                            "file {} exists".format(file))
             os.unlink(file)
 
     def test_put_files(self):

diff --git a/utils/SnapPy/METNO/Frost.py b/utils/SnapPy/METNO/Frost.py
@@ -1,25 +1,25 @@
 # SNAP: Servere Nuclear Accident Programme
 # Copyright (C) 1992-2017   Norwegian Meteorological Institute
-#
-# This file is part of SNAP. SNAP is free software: you can
-# redistribute it and/or modify it under the terms of the
-# GNU General Public License as published by the
+# 
+# This file is part of SNAP. SNAP is free software: you can 
+# redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the 
 # Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-#
+# 
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-#
+# 
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-"""
+'''
 Created on Nov 7, 2016
 
 @author: heikok
-"""
+'''
 import os
 from subprocess import TimeoutExpired
 from time import sleep
@@ -31,24 +31,22 @@
 
 
 class Frost(HPC):
-    """
+    '''
     Implementation of a HPC machine for frost.nsc.liu.se
-    """
+    '''
+
 
     def __init__(self):
-        """
+        '''
         Constructor
-        """
-        connection = SSHConnection(
-            username="metno_op", machine="frost.nsc.liu.se", port=22
-        )
+        '''
+        connection = SSHConnection(username="metno_op", machine="frost.nsc.liu.se", port=22)
         queue = SLURMQueue()
         super().__init__(connection, queue)
 
 
 class TestFrost(unittest.TestCase):
-    """tests for frost, only working when having an existing forecast account on frost"""
-
+    '''tests for frost, only working when having an existing forecast account on frost'''
     def setUp(self):
         unittest.TestCase.setUp(self)
         self.hpc = HPC.by_name("frost")
@@ -59,14 +57,15 @@ def setUp(self):
     def tearDown(self):
         unittest.TestCase.tearDown(self)
         for f in self.testFiles:
-            if os.path.exists(f):
+            if (os.path.exists(f)):
                 os.unlink(f)
 
     def test_connect(self):
         (out, error, retval) = self.hpc.syscall("echo", ["5"])
         self.assertEqual(retval, 0, "command succeeded")
         self.assertEqual(int(out), 5, "command output correct")
 
+
     def test_timeout(self):
         with self.assertRaises(TimeoutExpired):
             self.hpc.syscall("sleep", ["5"], timeout=1)
@@ -75,16 +74,15 @@ def test_full(self):
         status_file = os.path.join(self.rdir, "status")
         self.hpc.syscall("rm", ["-r", self.rdir])
         self.hpc.syscall("mkdir", ["-p", self.rdir])
-
+        
         for f in self.strangeFiles:
-            with open(f, "w") as fh:
+            with open(f, 'w') as fh:
                 fh.write(f)
             self.hpc.put_files([f], self.rdir)
             self.hpc.syscall("ls", [f])
-
+        
         with open(self.testFiles[0], "w") as fh:
-            fh.write(
-                """#! /bin/bash
+            fh.write('''#! /bin/bash
 
 #SBATCH -A met
 #SBATCH --nodes=1 --ntasks-per-node=1 --time=01:00:00
@@ -94,10 +92,7 @@ def test_full(self):
 
 sleep 8
 echo "finished" > {status}
-            """.format(
-                    status=status_file, rdir=self.rdir
-                )
-            )
+            '''.format(status=status_file, rdir=self.rdir))
         self.hpc.put_files([self.testFiles[0]], self.rdir)
         qjob = self.hpc.submit_job(os.path.join(self.rdir, self.testFiles[0]), [])
         self.assertIsNotNone(qjob, "job submitted")
@@ -122,6 +117,5 @@ def test_full(self):
 
         self.hpc.syscall("rm", ["-r", self.rdir])
 
-
 if __name__ == "__main__":
     unittest.main()