Merge pull request #34 from MiraGeoscience/release/0.1.6

merge Release/0.1.6 to main

Author: andrewg-mira

.github/workflows/issue_to_jira.yml

@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "param-sweeps"}]}'
     - name: Post JIRA link
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v3
       with:
         # The number of the issue or pull request in which to create a comment.
         issue-number: ${{ github.event.issue.number }}

.github/workflows/pr_add_jira_summary.yml

@@ -19,7 +19,7 @@ jobs:
         PR_TITLE: ${{ github.event.pull_request.title }}
       run: >
         echo $HEAD_REF $PR_TITLE
-        | echo "::set-output name=issue_key::$(grep -os "\b\(GA\|GEOPY\)-[0-9]\+" | head -n1)"
+        | echo "{issue_key}=$(grep -os "\b\(GA\|GEOPY\)-[0-9]\+" | head -n1)" >> "$GITHUB_OUTPUT"
     - name: Get JIRA summary
       id: get_jira_summary
       if: ${{ steps.find_jira_key.outputs.issue_key }}
@@ -31,7 +31,7 @@ jobs:
         -H "Authorization: Basic $JIRA_BASIC_AUTH"
         -H "Content-Type: application/json"
         "$JIRA_BASE_URL/rest/api/2/issue/${{ steps.find_jira_key.outputs.issue_key }}"
-        | echo "::set-output name=summary::$(jq -r '.fields.summary')"
+        | echo "summary=$(jq -r '.fields.summary')" >> "$GITHUB_OUTPUT"
     - name: Add comment
       if: ${{ steps.find_jira_key.outputs.issue_key }}
       env:

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.9.1
     hooks:
     -   id: black
         types: [text]
@@ -29,25 +29,30 @@ repos:
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
     -   id: flake8
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.13.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
+    rev: v1.5.1
     hooks:
     -   id: mypy
         additional_dependencies: [types-toml]
         args: [--ignore-missing-imports, --scripts-are-modules, --show-error-context,
                --show-column-numbers]
+-   repo: https://github.com/codingjoe/relint
+    rev: 3.1.0
+    hooks:
+    -   id: relint
+        args: [-W]  # to fail on warnings
 -   repo: local
     hooks:
     -   id: pylint
@@ -66,7 +71,7 @@ repos:
         types_or: [python, pyi]
         exclude: ^(devtools/|docs/|setup.py)
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
     -   id: codespell
         exclude: (\.ipynb$|^\.github/workflows/issue_to_jira.yml$)
@@ -89,7 +94,7 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
+    rev: v6.2.0
     hooks:
     -   id: rstcheck
         additional_dependencies: [sphinx]

.relint.yml

@@ -0,0 +1,10 @@
+- name: No import os.path
+  pattern: 'from os import\b.*\bpath\b'
+  hint: Use from pathlib import Path
+  filePattern: .*\.pyi?
+  error: false
+- name: No os.path
+  pattern: '\bos\.path\b'
+  hint: Use pathlib.Path
+  filePattern: .*\.pyi?
+  error: false

devtools/check-copyright.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #

param_sweeps/__init__.py

@@ -1,9 +1,9 @@
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #
 #  param-sweeps is distributed under the terms and conditions of the MIT License
 #  (see LICENSE file at the root of this source code package).
 
 
-__version__ = "0.1.5"
+__version__ = "0.1.6"

param_sweeps/constants.py

@@ -1,11 +1,15 @@
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #
 #  param-sweeps is distributed under the terms and conditions of the MIT License
 #  (see LICENSE file at the root of this source code package).
 
-default_ui_json = {
+from __future__ import annotations
+
+from typing import Any
+
+default_ui_json: dict[str, Any] = {
     "title": "Parameter sweep",
     "worker_uijson": None,
     "run_command": "param_sweeps.driver",

param_sweeps/driver.py

@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #
@@ -12,10 +12,11 @@
 import inspect
 import itertools
 import json
-import os
 import uuid
 from dataclasses import dataclass
 from inspect import signature
+from io import BytesIO
+from pathlib import Path
 from typing import Any
 
 import numpy as np
@@ -44,6 +45,9 @@ def from_input_file(cls, ifile: InputFile):
         cls_fields = list(signature(cls).parameters)
         base_params, app_params = {}, {}
 
+        if ifile.data is None:
+            raise ValueError("Input file data is empty.")
+
         for param, value in ifile.data.items():
             if param in cls_fields:
                 base_params[param] = value
@@ -92,10 +96,17 @@ def parameter_sets(self) -> dict:
 class SweepDriver:
     """Sweeps parameters of a worker driver."""
 
-    def __init__(self, params):
+    def __init__(self, params: SweepParams):
+        if params.geoh5 is None:
+            raise ValueError("Workspace must be specified.")
+
         self.params: SweepParams = params
-        self.workspace = params.geoh5
-        self.working_directory = os.path.dirname(self.workspace.h5file)
+        self.workspace: Workspace = params.geoh5
+
+        if isinstance(self.workspace.h5file, BytesIO) or self.workspace.h5file is None:
+            raise ValueError("Workspace must be saved to disk.")
+
+        self.working_directory = str(Path(self.workspace.h5file).parent)
         lookup = self.get_lookup()
         self.write_files(lookup)
 
@@ -126,8 +137,8 @@ def get_lookup(self):
 
     def update_lookup(self, lookup: dict, gather_first: bool = False):
         """Updates lookup with new entries. Ensures any previous runs are incorporated."""
-        lookup_path = os.path.join(self.working_directory, "lookup.json")
-        if os.path.exists(lookup_path) and gather_first:  # In case restarting
+        lookup_path = Path(self.working_directory) / "lookup.json"
+        if lookup_path.is_file() and gather_first:  # In case restarting
             with open(lookup_path, encoding="utf8") as file:
                 lookup.update(json.load(file))
 
@@ -145,10 +156,8 @@ def write_files(self, lookup):
                 if trial["status"] != "pending":
                     continue
 
-                filepath = os.path.join(
-                    os.path.dirname(workspace.h5file), f"{name}.ui.geoh5"
-                )
-                with Workspace(filepath) as iter_workspace:
+                filepath = Path(workspace.h5file).parent / f"{name}.ui.geoh5"
+                with Workspace.create(filepath) as iter_workspace:
                     ifile.data.update(
                         dict(
                             {key: val for key, val in trial.items() if key != "status"},
@@ -161,7 +170,7 @@ def write_files(self, lookup):
                             obj.copy(parent=iter_workspace, copy_children=True)
 
                 ifile.name = f"{name}.ui.json"
-                ifile.path = os.path.dirname(workspace.h5file)
+                ifile.path = str(Path(workspace.h5file).parent)
                 ifile.write_ui_json()
                 lookup[name]["status"] = "written"
 
@@ -170,13 +179,13 @@ def write_files(self, lookup):
     def run(self):
         """Execute a sweep."""
 
-        lookup_path = os.path.join(self.working_directory, "lookup.json")
+        lookup_path = Path(self.working_directory) / "lookup.json"
         with open(lookup_path, encoding="utf8") as file:
             lookup = json.load(file)
 
         for name, trial in lookup.items():
             ifile = InputFile.read_ui_json(
-                os.path.join(self.working_directory, f"{name}.ui.json")
+                Path(self.working_directory) / f"{name}.ui.json"
             )
             status = trial.pop("status")
             if status != "complete":
@@ -189,6 +198,8 @@ def run(self):
 
 def call_worker(ifile: InputFile):
     """Runs the worker for the sweep parameters contained in 'ifile'."""
+    if ifile.data is None:
+        raise ValueError("Input file data is empty.")
 
     run_cmd = ifile.data["run_command"]
     module = importlib.import_module(run_cmd)
@@ -204,9 +215,9 @@ def filt(member: Any) -> bool:
     driver.start(ifile.path_name)
 
 
-def file_validation(filepath):
+def file_validation(filepath: str | Path):
     """Validate file."""
-    if filepath.endswith("ui.json"):
+    if "".join(Path(filepath).suffixes) == ".ui.json":
         try:
             InputFile.read_ui_json(filepath)
         except BaseValidationError as err:
@@ -217,7 +228,7 @@ def file_validation(filepath):
         raise OSError(f"File argument {filepath} must have extension 'ui.json'.")
 
 
-def main(file_path):
+def main(file_path: str | Path):
     """Run the program."""
 
     file_validation(file_path)
@@ -234,4 +245,4 @@ def main(file_path):
     parser.add_argument("file", help="File with ui.json format.")
 
     args = parser.parse_args()
-    main(os.path.abspath(args.file))
+    main(Path(args.file).resolve(strict=True))

param_sweeps/generate.py

@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #
@@ -8,9 +8,9 @@
 from __future__ import annotations
 
 import argparse
-import os
 import re
 from copy import deepcopy
+from pathlib import Path
 
 from geoh5py.ui_json import InputFile
 
@@ -30,12 +30,10 @@ def generate(
     :param update_values: Updates for sweep files parameters
     """
 
-    file = os.path.abspath(worker)
-    ifile = InputFile.read_ui_json(file)
-    sweepfile = InputFile(
-        ui_json=deepcopy(default_ui_json), validation_options={"disabled": True}
-    )
-    sweepfile.data.update({"worker_uijson": worker})
+    file_path = Path(worker).resolve(strict=True)
+    ifile = InputFile.read_ui_json(file_path)
+    sweepfile = InputFile(ui_json=deepcopy(default_ui_json), validate=False)
+    sweepfile.data.update({"worker_uijson": str(worker)})
     if update_values:
         sweepfile.data.update(**update_values)
 
@@ -48,15 +46,15 @@ def generate(
             sweepfile.ui_json.update(forms)
 
     sweepfile.data["geoh5"] = ifile.data["geoh5"]
-    dirname = os.path.dirname(file)
-    filename = os.path.basename(file)
+    dirpath = file_path.parent
+    filename = file_path.name
     filename = filename.rstrip("ui.json")
     filename = re.sub(r"\._sweep$", "", filename)
     # filename = filename.rstrip("_sweep")
     filename = f"{filename}_sweep.ui.json"
 
-    print(f"Writing sweep file to: {os.path.join(dirname, filename)}")
-    sweepfile.write_ui_json(name=filename, path=dirname)
+    print(f"Writing sweep file to: {dirpath / filename}")
+    sweepfile.write_ui_json(name=filename, path=dirpath)
 
 
 def sweep_forms(param: str, value: int | float) -> dict:

param_sweeps/sample_driver.py

@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Mira Geoscience Ltd.
+#  Copyright (c) 2024 Mira Geoscience Ltd.
 #
 #  This file is part of param-sweeps.
 #