fix formatting

resources/generate_spec_files.py

@@ -66,6 +66,6 @@
         with open(header_file, 'a') as fo:
             fo.write(f'const std::string namespaces = R"delimiter(\n{json.dumps(ns_output, separators=(',', ':'))})delimiter";\n\n')
             fo.write('void registerVariables(std::map<std::string, const std::string*>& registry) {\n')
-            fo.write(''.join([f'    registry["{name.replace('_', '.')}"] = &{name};\n' for name in var_names]))
-            fo.write(f'    registry["namespace"] = &namespaces;\n')
+            fo.write(''.join([f'  registry["{name.replace('_', '.')}"] = &{name};\n' for name in var_names]))
+            fo.write(f'  registry["namespace"] = &namespaces;\n')
             fo.write(f'}};\n}}  // namespace AQNWB::spec::{ns['name'].replace('-', '_')}\n')

src/nwb/NWBFile.cpp

@@ -70,9 +70,14 @@ Status NWBFile::createFileStructure()
 
   io->createGroup("/specifications");
   io->createReferenceAttribute("/specifications", "/", ".specloc");
-  cacheSpecifications("core", spec::core::version, spec::core::registerVariables);
-  cacheSpecifications("hdmf-common", spec::hdmf_common::version, spec::hdmf_common::registerVariables);
-  cacheSpecifications("hdmf-experimental", spec::hdmf_experimental::version, spec::hdmf_experimental::registerVariables);
+  cacheSpecifications(
+      "core", spec::core::version, spec::core::registerVariables);
+  cacheSpecifications("hdmf-common",
+                      spec::hdmf_common::version,
+                      spec::hdmf_common::registerVariables);
+  cacheSpecifications("hdmf-experimental",
+                      spec::hdmf_experimental::version,
+                      spec::hdmf_experimental::registerVariables);
 
   std::string time = getCurrentTime();
   std::vector<std::string> timeVec = {time};
@@ -149,9 +154,10 @@ void NWBFile::stopRecording()
   io->stopRecording();
 }
 
-void NWBFile::cacheSpecifications(const std::string& specPath, 
-                                  const std::string& version,
-                                  void (*registerFunc)(std::map<std::string, const std::string*>&))
+void NWBFile::cacheSpecifications(
+    const std::string& specPath,
+    const std::string& version,
+    void (*registerFunc)(std::map<std::string, const std::string*>&))
 {
   std::map<std::string, const std::string*> registry;
   registerFunc(registry);
@@ -160,7 +166,8 @@ void NWBFile::cacheSpecifications(const std::string& specPath,
   io->createGroup("/specifications/" + specPath + "/" + version);
 
   for (const auto& [name, content] : registry) {
-      io->createStringDataSet("/specifications/" + specPath + "/" + version + "/" + name, *content);
+    io->createStringDataSet(
+        "/specifications/" + specPath + "/" + version + "/" + name, *content);
   }
 }
 

src/nwb/NWBFile.hpp

@@ -123,9 +123,10 @@ class NWBFile
    * @param registry The registry of specification files.
    * @param versionNumber The version number of the specification files.
    */
-  void cacheSpecifications(const std::string& specPath,
-                           const std::string& version, 
-                           void (*registerFunc)(std::map<std::string, const std::string*>&));
+  void cacheSpecifications(
+      const std::string& specPath,
+      const std::string& version,
+      void (*registerFunc)(std::map<std::string, const std::string*>&));
 
   /**
    * @brief Holds the Container (usually TimeSeries) objects that have been

src/spec/core.hpp

@@ -46,19 +46,20 @@ const std::string nwb_retinotopy = R"delimiter(
 const std::string namespaces = R"delimiter(
 {"namespaces":[{"name":"core","doc":"NWB namespace","author":["Andrew Tritt","Oliver Ruebel","Ryan Ly","Ben Dichter","Keith Godfrey","Jeff Teeters"],"contact":["[email protected]","[email protected]","[email protected]","[email protected]","[email protected]","[email protected]"],"full_name":"NWB core","schema":[{"namespace":"hdmf-common"},{"source":"nwb.base"},{"source":"nwb.device"},{"source":"nwb.epoch"},{"source":"nwb.image"},{"source":"nwb.file"},{"source":"nwb.misc"},{"source":"nwb.behavior"},{"source":"nwb.ecephys"},{"source":"nwb.icephys"},{"source":"nwb.ogen"},{"source":"nwb.ophys"},{"source":"nwb.retinotopy"}],"version":"2.7.0"}]})delimiter";
 
-void registerVariables(std::map<std::string, const std::string*>& registry) {
-    registry["nwb.base"] = &nwb_base;
-    registry["nwb.device"] = &nwb_device;
-    registry["nwb.epoch"] = &nwb_epoch;
-    registry["nwb.image"] = &nwb_image;
-    registry["nwb.file"] = &nwb_file;
-    registry["nwb.misc"] = &nwb_misc;
-    registry["nwb.behavior"] = &nwb_behavior;
-    registry["nwb.ecephys"] = &nwb_ecephys;
-    registry["nwb.icephys"] = &nwb_icephys;
-    registry["nwb.ogen"] = &nwb_ogen;
-    registry["nwb.ophys"] = &nwb_ophys;
-    registry["nwb.retinotopy"] = &nwb_retinotopy;
-    registry["namespace"] = &namespaces;
+void registerVariables(std::map<std::string, const std::string*>& registry)
+{
+  registry["nwb.base"] = &nwb_base;
+  registry["nwb.device"] = &nwb_device;
+  registry["nwb.epoch"] = &nwb_epoch;
+  registry["nwb.image"] = &nwb_image;
+  registry["nwb.file"] = &nwb_file;
+  registry["nwb.misc"] = &nwb_misc;
+  registry["nwb.behavior"] = &nwb_behavior;
+  registry["nwb.ecephys"] = &nwb_ecephys;
+  registry["nwb.icephys"] = &nwb_icephys;
+  registry["nwb.ogen"] = &nwb_ogen;
+  registry["nwb.ophys"] = &nwb_ophys;
+  registry["nwb.retinotopy"] = &nwb_retinotopy;
+  registry["namespace"] = &namespaces;
 };
 }  // namespace AQNWB::spec::core

src/spec/hdmf_common.hpp

@@ -19,10 +19,11 @@ const std::string sparse = R"delimiter(
 const std::string namespaces = R"delimiter(
 {"namespaces":[{"name":"hdmf-common","doc":"Common data structures provided by HDMF","author":["Andrew Tritt","Oliver Ruebel","Ryan Ly","Ben Dichter"],"contact":["[email protected]","[email protected]","[email protected]","[email protected]"],"full_name":"HDMF Common","schema":[{"source":"base"},{"source":"table"},{"source":"sparse"}],"version":"1.8.0"}]})delimiter";
 
-void registerVariables(std::map<std::string, const std::string*>& registry) {
-    registry["base"] = &base;
-    registry["table"] = &table;
-    registry["sparse"] = &sparse;
-    registry["namespace"] = &namespaces;
+void registerVariables(std::map<std::string, const std::string*>& registry)
+{
+  registry["base"] = &base;
+  registry["table"] = &table;
+  registry["sparse"] = &sparse;
+  registry["namespace"] = &namespaces;
 };
 }  // namespace AQNWB::spec::hdmf_common

src/spec/hdmf_experimental.hpp

@@ -16,9 +16,10 @@ const std::string resources = R"delimiter(
 const std::string namespaces = R"delimiter(
 {"namespaces":[{"name":"hdmf-experimental","doc":"Experimental data structures provided by HDMF. These are not guaranteed to be available in the future.","author":["Andrew Tritt","Oliver Ruebel","Ryan Ly","Ben Dichter","Matthew Avaylon"],"contact":["[email protected]","[email protected]","[email protected]","[email protected]","[email protected]"],"full_name":"HDMF Experimental","schema":[{"namespace":"hdmf-common"},{"source":"experimental"},{"source":"resources"}],"version":"0.5.0"}]})delimiter";
 
-void registerVariables(std::map<std::string, const std::string*>& registry) {
-    registry["experimental"] = &experimental;
-    registry["resources"] = &resources;
-    registry["namespace"] = &namespaces;
+void registerVariables(std::map<std::string, const std::string*>& registry)
+{
+  registry["experimental"] = &experimental;
+  registry["resources"] = &resources;
+  registry["namespace"] = &namespaces;
 };
 }  // namespace AQNWB::spec::hdmf_experimental