Improve error messages and fail if conda/virtualenv paths don't exist

Author: rkdarst

envkernel.py

@@ -13,6 +13,7 @@
 import subprocess
 import sys
 import tempfile
+import textwrap
 
 LOG = logging.getLogger('envkernel')
 LOG.setLevel(logging.INFO)
@@ -242,11 +243,12 @@ def install_kernel(self, kernel, name, user=False, replace=None, prefix=None, lo
                 user=user, replace=replace, prefix=prefix)
 
         LOG.info("")
+        LOG.info("  Kernel command: %s", kernel['argv'])
         try:
-            LOG.info("  Kernel saved to {}".format(jupyter_client.kernelspec.KernelSpecManager().get_kernel_spec(name).resource_dir))
+            LOG.info("  Success: Kernel saved to {}".format(jupyter_client.kernelspec.KernelSpecManager().get_kernel_spec(name).resource_dir))
         except jupyter_client.kernelspec.NoSuchKernel:
             LOG.info("  Note: Kernel not detected with current search path.")
-        LOG.info("  Command line: %s", kernel['argv'])
+        #LOG.info("  Kernel file:\n%s", textwrap.indent(json.dumps(kernel, sort_keys=True, indent=1), '    '))
 
     def run(self):
         """Hook that gets run before kernel invoked"""
@@ -322,22 +324,48 @@ def setup(self):
         args, unknown_args = parser.parse_known_args(self.argv)
 
         kernel = self.get_kernel()
+        path = args.path
+        path = os.path.abspath(path)
         kernel['argv'] = [
             os.path.realpath(sys.argv[0]),
             self.__class__.__name__, 'run',
             *unknown_args,
-            args.path,
+            path,
             '--',
             *kernel['argv'],
         ]
         if 'display_name' not in kernel:
             kernel['display_name'] = "{} ({}, {})".format(
             os.path.basename(args.path.strip('/')),
             self.__class__.__name__,
-            args.path)
+            path)
+        if args.path != 'TESTTARGET':  # un-expanded
+            if not os.path.exists(path):
+                print(self.notfound_message%(self.__class__.__name__, path))
+                LOG.critical("ERROR: %s does not exist: %s", self.__class__.__name__, path)
+                sys.exit(1)
+            if not os.path.exists(pjoin(path, 'bin')):
+                print(self.notfound_message%(self.__class__.__name__, path+'/bin'))
+                LOG.critical("ERROR: %s bin does not exist: %s/bin", self.__class__.__name__, path)
+                sys.exit(1)
         self.install_kernel(kernel, name=self.name, user=self.user,
                             replace=self.replace, prefix=self.prefix)
 
+    notfound_message = """\
+ERROR: %s path does not exist: %s
+
+You need to give a path to the environment, not just the name.  (A
+relative path gets expanded to an absolute path.)
+
+For conda, you can get this from:
+  conda env list
+
+If it's a conda environment and it is activated, you can use
+$CONDA_PREFIX like such:
+  envkernel conda [other arguments] $CONDA_PREFIX
+"""
+
+
     def run(self):
         """load modules and run:
 
@@ -385,6 +413,12 @@ def _run(self, args, rest):
             os.environ['PS1'] = "(venv3) " + os.environ['PS1']
 
         self.execvp(rest[0], rest)
+    notfound_message = """\
+ERROR: %s path does not exist: %s
+
+You need to give a path to the environment, not just the name.  A
+relative path gets expanded to an absolute path.
+"""
 
 
 
@@ -533,12 +567,13 @@ def setup(self):
         LOG.debug('setup: remaining args: %s', unknown_args)
 
         kernel = self.get_kernel()
+        image = os.path.abspath(args.image)
         kernel['argv'] = [
             os.path.realpath(sys.argv[0]),
             'singularity', 'run',
             '--connection-file', '{connection_file}',
             #*[ '--mount={}'.format(x) for x in args.mount],
-            args.image,
+            image,
             *unknown_args,
             '--',
             *kernel['argv'],

test_envkernel.py

@@ -94,21 +94,21 @@ def is_sublist(list_, sublist):
 
 @all_modes()
 def test_basic(d, mode):
-    kern = install(d, "%s MOD1"%mode)
+    kern = install(d, "%s TESTTARGET"%mode)
     #assert kern['argv'][0] == 'envkernel'  # defined above
     assert kern['ek'][1:3] == [mode, 'run']
 
 @all_modes()
 def test_display_name(d, mode):
-    kern = install(d, "%s --display-name=AAA MOD1"%mode)
+    kern = install(d, "%s --display-name=AAA TESTTARGET"%mode)
     assert kern['kernel']['display_name'] == 'AAA'
 
 @all_modes(['conda'])
 def test_template(d, mode):
     os.environ['JUPYTER_PATH'] = pjoin(d, 'share/jupyter')
     subprocess.call("python -m ipykernel install --name=aaa-ipy --display-name=BBB --prefix=%s"%d, shell=True)
     #os.environ['ENVKERNEL_TESTPATH'] = os.path.join(d, 'share/jupyter/kernels')
-    kern = install(d, "%s --kernel-template aaa-ipy MOD1"%mode)
+    kern = install(d, "%s --kernel-template aaa-ipy TESTTARGET"%mode)
     assert kern['kernel']['display_name'] == 'BBB'
 
 @all_modes(['conda'])
@@ -118,7 +118,7 @@ def test_template_copyfiles(d, mode):
     f = open(pjoin(d, 'share/jupyter/kernels/', 'aaa-ipy', 'A.txt'), 'w')
     f.write('LMNO')
     f.close()
-    kern = install(d, "%s --kernel-template aaa-ipy MOD1"%mode)
+    kern = install(d, "%s --kernel-template aaa-ipy TESTTARGET"%mode)
     assert os.path.exists(pjoin(kern['dir'], 'A.txt'))
     assert open(pjoin(kern['dir'], 'A.txt')).read() == 'LMNO'
 
@@ -127,10 +127,10 @@ def test_template_make_path_relative(d, mode):
     os.environ['JUPYTER_PATH'] = pjoin(d, 'share/jupyter')
     subprocess.call("python -m ipykernel install --name=aaa-ipy --display-name=BBB --prefix=%s"%d, shell=True)
     # First test it without, ensure it has the full path
-    kern = install(d, "%s --kernel-template aaa-ipy MOD1"%mode)
+    kern = install(d, "%s --kernel-template aaa-ipy TESTTARGET"%mode)
     assert kern['k'][0] != 'python' # This is an absolete path
     # Now test it with --kernel-make-path-relative and ensure it's relative
-    kern = install(d, "%s --kernel-template aaa-ipy --kernel-make-path-relative MOD1"%mode)
+    kern = install(d, "%s --kernel-template aaa-ipy --kernel-make-path-relative TESTTARGET"%mode)
     assert kern['k'][0] == 'python' # This is an absolete path
 
 def test_help():
@@ -148,7 +148,7 @@ def test_logging(d, caplog):
     Run first without -v and make sure some stuff isn't printed.
     Then, run with -v and ensure that the argument processing is output.
     """
-    cmd = "python3 -m envkernel lmod --name=ABC --display-name=AAA MOD1 --prefix=%s"%d
+    cmd = "python3 -m envkernel lmod --name=ABC --display-name=AAA LMOD --prefix=%s"%d
     print(d)
     env = os.environ.copy()
     env['JUPYTER_PATH'] = pjoin(d, 'share/jupyter')
@@ -160,7 +160,7 @@ def test_logging(d, caplog):
     print(stdout)
     assert 'Namespace' not in stdout
     assert 'kernel-specific' not in stdout
-    assert 'Command line:' in stdout
+    assert 'Kernel command:' in stdout
     # Now test verbose (should have some debugging info)
     p = subprocess.Popen(cmd+' -v', env=env,
                          shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
@@ -169,37 +169,37 @@ def test_logging(d, caplog):
     #print(stdout)
     assert 'Namespace' in stdout
     assert 'kernel-specific' in stdout
-    assert 'Command line:' in stdout
+    assert 'Kernel command:' in stdout
 
 def test_umask(d):
     orig_umask = os.umask(0)
     # Test multiple umasks, and kerneldir + kernel.json
     for umask in [0, 0o022]:
         os.umask(umask)
-        kern = install(d, "lmod MOD1")
+        kern = install(d, "lmod TESTTARGET")
         assert os.stat(kern['dir']).st_mode & 0o777  ==  0o777&(~umask)
         assert os.stat(pjoin(kern['dir'], 'kernel.json')).st_mode & 0o777  ==  0o666&(~umask)
     os.umask(orig_umask)
 
 
 @all_modes()
 def test_set_python(d, mode):
-    kern = install(d, "%s --python=AAA MOD1"%mode)
+    kern = install(d, "%s --python=AAA TESTTARGET"%mode)
     assert kern['k'][0] == 'AAA'
 
 @all_modes()
 def test_set_kernel_cmd(d, mode):
-    kern = install(d, "%s --kernel-cmd='a b c d' MOD1"%mode)
+    kern = install(d, "%s --kernel-cmd='a b c d' TESTTARGET"%mode)
     assert kern['k'] == ['a', 'b', 'c', 'd']
 
 @all_modes()
 def test_language(d, mode):
-    kern = install(d, "%s --language=AAA MOD1"%mode)
+    kern = install(d, "%s --language=AAA TESTTARGET"%mode)
     assert kern['kernel']['language'] == 'AAA'
 
 @all_modes()
 def test_env(d, mode):
-    kern = install(d, "%s --env=AAA=BBB --env=CCC=DDD MOD1"%mode)
+    kern = install(d, "%s --env=AAA=BBB --env=CCC=DDD TESTTARGET"%mode)
     assert kern['kernel']['env']['AAA'] == 'BBB'
     assert kern['kernel']['env']['CCC'] == 'DDD'
 
@@ -234,28 +234,28 @@ def test_exec(_file, _args):
 @all_modes()
 def test_default_language(d, mode):
     # default language is ipykernel
-    kern = install(d, "%s MOD1"%mode)
+    kern = install(d, "%s TESTTARGET"%mode)
     assert kern['kernel']['language'] == 'python'
     assert kern['k'][0] == 'python'
     assert kern['k'][1:4] == ['-m', 'ipykernel_launcher', '-f']
 
 @all_modes()
 def test_ipykernel(d, mode):
-    kern = install(d, "%s --kernel=ipykernel MOD1"%mode)
+    kern = install(d, "%s --kernel=ipykernel TESTTARGET"%mode)
     assert kern['kernel']['language'] == 'python'
     assert kern['k'][0] == 'python'
     assert kern['k'][1:4] == ['-m', 'ipykernel_launcher', '-f']
 
 @all_modes()
 def test_ir(d, mode):
-    kern = install(d, "%s --kernel=ir MOD1"%mode)
+    kern = install(d, "%s --kernel=ir TESTTARGET"%mode)
     assert kern['kernel']['language'] == 'R'
     assert kern['k'][0] == 'R'
     assert kern['k'][1:5] == ['--slave', '-e', 'IRkernel::main()', '--args']
 
 @all_modes()
 def test_imatlab(d, mode):
-    kern = install(d, "%s --kernel=imatlab MOD1"%mode)
+    kern = install(d, "%s --kernel=imatlab TESTTARGET"%mode)
     assert kern['kernel']['language'] == 'matlab'
     assert kern['k'][0].endswith('python')
     assert kern['k'][1:4] == ['-m', 'imatlab', '-f']
@@ -277,29 +277,29 @@ def test_lmod_purge(d):
     assert kern['ek'][-1] == 'MOD3'
 
 def test_conda(d):
-    kern = install(d, "conda /PATH/BBB")
+    kern = install(d, "conda TESTTARGET")
     #assert kern['argv'][0] == 'envkernel'  # defined above
     assert kern['ek'][1:3] == ['conda', 'run']
-    assert kern['ek'][-1] == '/PATH/BBB'
+    assert kern['ek'][-1].endswith('TESTTARGET')
 
 def test_virtualenv(d):
-    kern = install(d, "virtualenv /PATH/CCC")
+    kern = install(d, "virtualenv TESTTARGET")
     #assert kern['argv'][0] == 'envkernel'  # defined above
     assert kern['ek'][1:3] == ['virtualenv', 'run']
-    assert kern['ek'][-1] == '/PATH/CCC'
+    assert kern['ek'][-1].endswith('TESTTARGET')
 
 def test_docker(d):
-    kern = install(d, "docker --some-arg=AAA IMAGE1")
+    kern = install(d, "docker --some-arg=AAA TESTIMAGE")
     #assert kern['argv'][0] == 'envkernel'  # defined above
     assert kern['ek'][1:3] == ['docker', 'run']
-    assert kern['ek'][-2] == 'IMAGE1'
+    assert kern['ek'][-2] == 'TESTIMAGE'
     assert '--some-arg=AAA' in kern['ek']
 
 def test_singularity(d):
-    kern = install(d, "singularity --some-arg=AAA /PATH/TO/IMAGE2")
+    kern = install(d, "singularity --some-arg=AAA /PATH/TO/TESTIMAGE2")
     #assert kern['argv'][0] == 'envkernel'  # defined above
     assert kern['ek'][1:3] == ['singularity', 'run']
-    assert kern['ek'][-2] == '/PATH/TO/IMAGE2'
+    assert kern['ek'][-2] == '/PATH/TO/TESTIMAGE2'
     assert '--some-arg=AAA' in kern['ek']
 
 
@@ -369,7 +369,7 @@ def test_run_singularity(d):
     def test_exec(_file, argv):
         assert argv[0] == 'singularity'
         assert '--some-arg=AAA' in argv
-        assert 'IMAGE' in argv
+        assert os.path.join(os.getcwd(), 'IMAGE') in argv
     kern = install(d, "singularity --some-arg=AAA IMAGE")
     run(d, kern, test_exec)