hotfix: revise porting to Loader

oesteban · Mar 19, 2024 · 21cc46c · 21cc46c
1 parent 1d993d8
commit 21cc46c
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Showing 4 changed files with 14 additions and 14 deletions.
diff --git a/mriqc/data/config.py b/mriqc/data/config.py
@@ -37,7 +37,7 @@ class GroupTemplate:
     def __init__(self):
         import jinja2
 
-        self.template_str = Loader("mriqc")("data/reports/group.html")
+        self.template_str = Loader(__package__)("reports/group.html").absolute()
         self.env = jinja2.Environment(
             loader=jinja2.FileSystemLoader(searchpath="/"),
             trim_blocks=True,
@@ -46,7 +46,7 @@ def __init__(self):
 
     def compile(self, configs):
         """Generates a string with the replacements"""
-        template = self.env.get_template(self.template_str)
+        template = self.env.get_template(str(self.template_str))
         return template.render(configs)
 
     def generate_conf(self, configs, path):

diff --git a/mriqc/interfaces/common/ensure_size.py b/mriqc/interfaces/common/ensure_size.py
@@ -147,7 +147,7 @@ def _run_interface(self, runtime):
                 input_image=self.inputs.in_file,
                 reference_image=REF_FILE_NAME,
                 interpolation="LanczosWindowedSinc",
-                transforms=[load_data("data/itk_identity.tfm")],
+                transforms=[str(load_data("data/itk_identity.tfm").absolute())],
                 output_image=out_file,
             ).run()
 
@@ -168,7 +168,7 @@ def _run_interface(self, runtime):
                     input_image=self.inputs.in_mask,
                     reference_image=REF_MASK_NAME,
                     interpolation="NearestNeighbor",
-                    transforms=[load_data("data/itk_identity.tfm")],
+                    transforms=[str(load_data("data/itk_identity.tfm").absolute())],
                     output_image=out_mask,
                 ).run()
 

diff --git a/mriqc/reports/group.py b/mriqc/reports/group.py
@@ -267,15 +267,15 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
             "version": ver,
             "csv_groups": csv_groups,
             "failed": failed,
-            "boxplots_js": open(
-                load_data("data/reports/embed_resources/boxplots.js"),
-            ).read(),
-            "d3_js": open(
-                load_data("data/reports/embed_resources/d3.min.js"),
-            ).read(),
-            "boxplots_css": open(
-                load_data("data/reports/embed_resources/boxplots.css"),
-            ).read(),
+            "boxplots_js": load_data(
+                "data/reports/embed_resources/boxplots.js"
+            ).read_text(),
+            "d3_js": load_data(
+                "data/reports/embed_resources/d3.min.js"
+            ).read_text(),
+            "boxplots_css": load_data(
+                "data/reports/embed_resources/boxplots.css"
+            ).read_text(),
         },
         out_file,
     )

diff --git a/mriqc/testing.py b/mriqc/testing.py
@@ -36,7 +36,7 @@ def mock_config():
     """Create a mock config for documentation and testing purposes."""
     from . import config
 
-    filename = Path(_load_data("data/config-example.toml"))
+    filename = _load_data("data/config-example.toml")
     settings = loads(filename.read_text())
     for sectionname, configs in settings.items():
         if sectionname != "environment":