Merge pull request #27 from brainglobe/smg/tests-refactor

Refactor tests

MANIFEST.in

@@ -6,17 +6,18 @@ exclude *.yaml
 exclude *.yml
 exclude Dockerfile
 exclude *.ini
-exclude asv.conf.json
-exclude brainglobe_workflows/cellfinder/default_config.json
 
 recursive-include brainglobe_workflows *.py
+recursive-include brainglobe_workflows/configs *.json
+recursive-include brainglobe_benchmarks *.py
+recursive-exclude brainglobe_benchmarks/results *
+include asv.conf.json
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 global-include *.pxd
 
-prune benchmarks
 prune docs
 prune tests
 prune resources

asv.conf.json

@@ -11,7 +11,8 @@
 
     // The URL or local path of the source code repository for the
     // project being benchmarked
-    "repo": ".",
+    // "repo": ".",
+    "repo": "https://github.com/brainglobe/brainglobe-workflows",
 
     // The Python project's subdirectory in your repo.  If missing or
     // the empty string, the project is assumed to be located at the root
@@ -39,14 +40,14 @@
 
     // List of branches to benchmark. If not provided, defaults to "master"
     // (for git) or "default" (for mercurial).
-    "branches": ["main"], // for git
+    "branches": ["smg/tests-refactor"], // for git
     // "branches": ["default"],    // for mercurial
 
     // The DVCS being used.  If not set, it will be automatically
     // determined from "repo" by looking at the protocol in the URL
     // (if remote), or by looking for special directories, such as
     // ".git" (if local).
-    // "dvcs": "git",
+    "dvcs": "git",
 
     // The tool to use to create environments.  May be "conda",
     // "virtualenv", "mamba" (above 3.8)
@@ -146,19 +147,19 @@
 
     // The directory (relative to the current directory) that benchmarks are
     // stored in.  If not provided, defaults to "benchmarks"
-    // "benchmark_dir": "benchmarks",
+    "benchmark_dir": "brainglobe_benchmarks",
 
     // The directory (relative to the current directory) to cache the Python
     // environments in.  If not provided, defaults to "env"
     "env_dir": ".asv/env",
 
     // The directory (relative to the current directory) that raw benchmark
     // results are stored in.  If not provided, defaults to "results".
-    "results_dir": "benchmarks/results",
+    "results_dir": "brainglobe_benchmarks/results",
 
     // The directory (relative to the current directory) that the html tree
     // should be written to.  If not provided, defaults to "html".
-    "html_dir": "benchmarks/html",
+    "html_dir": "brainglobe_benchmarks/html",
 
     // The number of characters to retain in the commit hashes.
     // "hash_length": 8,

benchmarks/cellfinder.py → brainglobe_benchmarks/cellfinder.py

@@ -7,14 +7,12 @@
 from cellfinder_core.main import main as cellfinder_run
 from cellfinder_core.tools.IO import read_with_dask
 
-from brainglobe_workflows.cellfinder.cellfinder_main import (
-    DEFAULT_JSON_CONFIG_PATH,
+from brainglobe_workflows.cellfinder import (
     CellfinderConfig,
     run_workflow_from_cellfinder_run,
 )
-from brainglobe_workflows.cellfinder.cellfinder_main import (
-    setup as setup_cellfinder_workflow,
-)
+from brainglobe_workflows.cellfinder import setup as setup_cellfinder_workflow
+from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
 
 
 class TimeBenchmarkPrepGIN:
@@ -79,7 +77,7 @@ class TimeBenchmarkPrepGIN:
     min_run_count = 2  # default:2
 
     # Custom attributes
-    input_config_path = str(DEFAULT_JSON_CONFIG_PATH)
+    input_config_path = str(DEFAULT_JSON_CONFIG_PATH_CELLFINDER)
 
     def setup_cache(
         self,
@@ -114,7 +112,7 @@ def setup_cache(
             known_hash=config.data_hash,
             path=config.install_path,
             progressbar=True,
-            processor=pooch.Unzip(extract_dir=config.extract_dir_relative),
+            processor=pooch.Unzip(extract_dir=config.data_dir_relative),
         )
 
         # Check paths to input data should now exist in config