Make output directory when it didn't exist for workflow (#290)

- Workflow base class will now create output folder if it doesn't exist (see also
   alchemistry/flamel#24 )
- add test
- update CHANGES

CHANGES

@@ -13,6 +13,14 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" https://semver.org
 
 ------------------------------------------------------------------------------
+
+*/*/* xiki-tempula, orbeckst
+
+  * 2.0.0
+
+Enhancements
+  - The output folder will be created if not existed in workflows (PR #290).
+
 12/09/2022 DrDomenicoMarson, xiki-tempula, orbeckst
 
   * 1.0.1

src/alchemlyb/tests/test_workflow.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 
 import pandas as pd
 import pytest
@@ -10,11 +11,14 @@ class Test_automatic_base:
     @staticmethod
     @pytest.fixture(scope="session")
     def workflow(tmp_path_factory):
-        outdir = tmp_path_factory.mktemp("out")
+        outdir = tmp_path_factory.mktemp("out") / "abc" / "def"
         workflow = base.WorkflowBase(out=str(outdir))
         workflow.run()
         return workflow
 
+    def test_outdir(self, workflow):
+        assert Path(workflow.out).is_dir()
+
     def test_write(self, workflow):
         """Patch the output directory to tmpdir"""
         workflow.result.to_pickle(os.path.join(workflow.out, "result.pkl"))

src/alchemlyb/workflows/abfe.py

@@ -8,7 +8,6 @@
 import pandas as pd
 
 from .base import WorkflowBase
-from .. import __version__
 from .. import concat
 from ..convergence import forward_backward_convergence
 from ..estimators import AutoMBAR as MBAR
@@ -75,16 +74,9 @@ def __init__(
         suffix="xvg",
         outdirectory=os.path.curdir,
     ):
-
         super().__init__(units, software, T, outdirectory)
-        self.logger = logging.getLogger("alchemlyb.workflows.ABFE")
         self.logger.info("Initialise Alchemlyb ABFE Workflow")
-        self.logger.info(f"Alchemlyb Version: f{__version__}")
-        self.logger.info(f"Set Temperature to {T} K.")
-        self.logger.info(f"Set Software to {software}.")
-
         self.update_units(units)
-
         self.logger.info(
             f"Finding files with prefix: {prefix}, suffix: "
             f"{suffix} under directory {dir} produced by "
@@ -105,6 +97,9 @@ def __init__(
         else:
             raise NotImplementedError(f"{software} parser not found.")
 
+    def _logger_setup(self):
+        self.logger = logging.getLogger("alchemlyb.workflows.ABFE")
+
     def read(self, read_u_nk=True, read_dHdl=True):
         """Read the u_nk and dHdL data from the
         :attr:`~alchemlyb.workflows.ABFE.file_list`

src/alchemlyb/workflows/base.py

@@ -1,7 +1,12 @@
 """Basic building blocks for free energy workflows."""
 
+import logging
+from pathlib import Path
+
 import pandas as pd
 
+from .. import __version__
+
 
 class WorkflowBase:
     """The base class for the Workflow.
@@ -42,11 +47,21 @@ class WorkflowBase:
     def __init__(
         self, units="kT", software="Gromacs", T=298, out="./", *args, **kwargs
     ):
+        self._logger_setup()
+        self.logger.info(f"Alchemlyb Version: f{__version__}")
+        self.logger.info(f"Set Temperature to {T} K.")
         self.T = T
+        self.logger.info(f"Set Software to {software}.")
         self.software = software
         self.unit = units
         self.file_list = []
         self.out = out
+        if not Path(out).is_dir():
+            self.logger.info(f"Make output folder {out}.")
+            Path(out).mkdir(parents=True)
+
+    def _logger_setup(self):
+        self.logger = logging.getLogger("alchemlyb.workflows.WorkflowBase")
 
     def run(self, *args, **kwargs):
         """Run the workflow in an automatic fashion.