Upgrading Aurora to AiiDA 2.x

.github/workflows/ci.yml

@@ -43,7 +43,6 @@ jobs:
       run: |
         pip install --upgrade pip
         pip install -e .[testing]
-        reentry scan -r aiida
 
     - name: Run test suite
       env:
@@ -65,7 +64,6 @@ jobs:
       run: |
         pip install --upgrade pip
         pip install -e .[docs]
-        reentry scan -r aiida
     - name: Build docs
       run: cd docs && make
 
@@ -82,7 +80,6 @@ jobs:
       run: |
         pip install --upgrade pip
         pip install -e .[pre-commit,docs,testing]
-        reentry scan -r aiida
     - name: Run pre-commit
       run: |
         pre-commit install

aiida_aurora/calculations/cycler.py

@@ -94,7 +94,7 @@ def prepare_for_submission(self, folder):
         """
 
         # if connecting to a Windows PowerShell computer, change the extension of the submit script to '.ps1'
-        if self.inputs.code.computer.transport_type == "sshtowin":
+        if self.inputs.code.computer.transport_type == "ssh2win":
             submit_script_filename = self.node.get_option("submit_script_filename")
             if not submit_script_filename.endswith(".ps1"):
                 if submit_script_filename.endswith(".sh"):

aiida_aurora/scheduler.py

@@ -144,7 +144,11 @@ def _get_submit_script_header(self, job_tmpl):
         :param job_tmpl: a ``JobTemplate`` instance with relevant parameters set.
         """
         # set the `_shell_cmd` class attribute from the job template
-        TomatoScheduler._shell_cmd = job_tmpl.shell_type
+        # FIXME shell_type used to be job_tmpl.shell_type, which was added to
+        # aiida-core's `JobTemplate` class by Loris. Awaiting resolution.
+        shell_type = "powershell"
+        # shell_type = "bash"  # uncomment when debugging on Linux
+        TomatoScheduler._shell_cmd = shell_type
         self._logger.debug(f"_get_submit_script_header: _shell_cmd: {self._shell_cmd}")
 
         import string
@@ -155,14 +159,14 @@ def _get_submit_script_header(self, job_tmpl):
             job_title = re.sub(r"[^a-zA-Z0-9_.-]+", "", job_tmpl.job_name)
 
             # prepend a 'j' (for 'job') before the string if the string
-            # is now empty or does not start with a valid charachter
+            # is now empty or does not start with a valid character
             if not job_title or (job_title[0] not in string.ascii_letters + string.digits):
                 job_title = f"j{job_title}"
 
             # Truncate to the first 128 characters
             # Nothing is done if the string is shorter.
             job_title = job_title[:128]
-            if job_tmpl.shell_type == "powershell":
+            if shell_type == "powershell":
                 header = f"$JOB_TITLE='{job_title}'"
             else:
                 header = f"JOB_TITLE='{job_title}'"
@@ -342,7 +346,8 @@ def _parse_submit_output(self, retval, stdout, stderr):
         stdout_dict = yaml.full_load(stdout)
         if "jobid" in stdout_dict:
             self._logger.debug(f"The submitted jobid is {stdout_dict['jobid']}")
-            return stdout_dict["jobid"]
+            # HACK did not need to str-cast prior to aiida 2.x upgrade
+            return str(stdout_dict["jobid"])
 
         # If I am here, no jobid was found
         self.logger.error(f"in _parse_submit_output: unable to find the job id: {stdout}")