support gzipped json files

src/openfecli/commands/gather.py

@@ -8,6 +8,7 @@
 
 import click
 import pandas as pd
+from gufe.utils import magic_open
 
 from openfecli import OFECommandPlugin
 from openfecli.clicktypes import HyphenAwareChoice
@@ -178,7 +179,10 @@ def format_df_with_precision(
 
 def is_results_json(fpath: os.PathLike | str) -> bool:
     """Sanity check that file is a result json before we try to deserialize"""
-    return "estimate" in open(fpath, "r").read(20)
+
+    with open(fpath, "rb") as raw:
+        with magic_open(raw) as f:
+            return "estimate" in f.read(20)
 
 
 def load_json(fpath: os.PathLike | str) -> dict:
@@ -201,7 +205,9 @@ def load_json(fpath: os.PathLike | str) -> dict:
 
     from gufe.tokenization import JSON_HANDLER
 
-    return json.load(open(fpath, "r"), cls=JSON_HANDLER.decoder)
+    with open(fpath, "rb") as raw:
+        with magic_open(raw) as f:
+            return json.load(f, cls=JSON_HANDLER.decoder)
 
 
 def _get_names(result: dict) -> tuple[str, str]:
@@ -609,17 +615,13 @@ def _collect_result_jsons(results: List[os.PathLike | str]) -> List[pathlib.Path
     def collect_jsons(results: List[os.PathLike]):
         all_jsons = []
         for p in results:
-            if str(p).endswith("json"):
+            if ".json" in str(p):
                 all_jsons.append(p)
             elif p.is_dir():
-                all_jsons.extend(glob.glob(f"{p}/**/*json", recursive=True))
+                all_jsons.extend(glob.glob(f"{p}/**/*.json*", recursive=True))
 
         return all_jsons
 
-    def is_results_json(fpath: os.PathLike | str) -> bool:
-        """Sanity check that file is a result json before we try to deserialize"""
-        return "estimate" in open(fpath, "r").read(20)
-
     results = sorted(results)  # ensures reproducible output order regardless of input order
 
     # 1) find all possible jsons
@@ -774,7 +776,7 @@ def gather(
     RESULTS is the path(s) to JSON files or directories of JSON files containing RBFE protocol results as generated by ``openfe quickrun``.
 
     All directories will be walked recursively and any valid JSON results files will be gathered.
-    Files must end in .json to be collected, and invalid files will be ignored.
+    Files must contain `".json"` to be collected, and invalid files will be ignored.
 
     The results reported depends on ``--report`` flag:
 

src/openfecli/tests/commands/test_gather.py

@@ -515,13 +515,6 @@ def septop_result_dir(tmp_path_factory) -> pathlib.Path:
     ZENODO_SEPTOP_DATA.fetch("septop_results.zip", processor=pooch.Unzip())
     result_dir = pathlib.Path(POOCH_CACHE) / "septop_results.zip.unzip/septop_results/"
 
-    for gz_file in result_dir.rglob("*.json.gz"):
-        json_file = gz_file.with_suffix("")  # removes .gz, leaving .json
-        with gzip.open(gz_file, "rb") as f_in:
-            with open(json_file, "wb") as f_out:
-                f_out.write(f_in.read())
-        gz_file.unlink()  # remove the .gz file
-
     return result_dir