V1 release #49

dgasmith · 2018-05-22T13:07:22Z

Description

This PR aims to provide the necessary infrastructure and schema improvements to have a version 1 release, see #47. This version 1 is by no means feature complete, but aims to give a scaffold to build off of. Enumerated changes:

Moved the Python module to "qcschema" to match python module style changes.
Changed the name of the schema from QC_JSON to qc_schema to match style choices and current naming directions.
Created three separate schema qc_schema_input, qc_schema_output, qc_schema_molecule to better reflect what each of these objects are.
Minted "v1" of the schema and added code infrastructure to support querying of different schema
Moved several pieces of documentation around to make the repo a bit cleaner and changed some working in the docs to better label topics.

Questions

Thinking on multiple resulting schema for a moment, does this make sense? I find it hard to have a single schema where difference pieces are used in separate settings and I have not found a good consensus online. This also opens us up to have additional schema like geometry optimization results as discussed in Multiple conformations in a single file? #34.
Is there anything else that must go in version 1?

TODO

Mint GitHub tag and release.
Update permanent URL's to individual schema.

Status

Ready to go

…style conventions

loriab

I think the pieces (mol, input, output, w/output incl. input) are orthogonal enough that separately named/versioned schemas are a good idea.

loriab · 2018-05-24T16:27:03Z

qcschema/dev/dev_schema.py

-    "name": "QC_JSON",
-    "version": "0.1.dev",
-    "url": "http://schema_host.org/schemas/0/something.schema",
+    "$schema": "http://json-schema.org/draft-04/schema#",


why use draft-04, not 06? from my uninformed view, the 06 changes (http://json-schema.org/draft-06/json-schema-release-notes.html) look pretty good.

I do not believe we use anything in 6 at the moment, so might as well back down the compatibility requirements until we do.

Ok, we'll just be on-guard for any field names involving id.

loriab · 2018-05-24T16:29:21Z

qcschema/dev/dev_schema.py

-    "url": "http://schema_host.org/schemas/0/something.schema",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "name": "qc_schema_input",
+    "version": "dev",


wouldn't hurt to make this 1.dev, so at least one knows what version you're approaching. scrupulously, this should be 1.devN where N is git commits past 0 tag, but 1.dev will do. :-)

Sure, fixed. I didn't add versioner or the like to keep it with the simple versioning philosophy.

loriab · 2018-05-24T16:30:42Z

qcschema/dev/dev_schema.py

    "description": "The MolSSI Quantum Chemistry Schema",
    "type": "object",
    "properties": {
        "molecule": molecule.molecule,
        "schema_name": {
            "type": "string",
-            "pattern": "\W*(QC_JSON)\W*"
+            "pattern": "\W*(qc_schema)\W*"


why qcschema in docs and dir structure and qc_schema elsewhere? I'm glad of the change from QC_JSON, both in caps and name.

qcschema is canonical Python for modules (I dont think this is in the docs?) while qc_schema is the keyword snake case.

Thanks for the distinction – makes much more sense now. (reference to docs was the sphinxproj name.)

loriab · 2018-05-24T16:35:36Z

qcschema/dev/molecule.py

+    "name": "qc_schema_molecule",
+    "version": "dev",
+    "description": "The MolSSI Quantum Chemistry Molecular Schema",
+    "type": "object",


below at https://github.com/MolSSI/QC_JSON_Schema/pull/49/files#diff-fb40813be873a1ea003de289cb1f9373R59, length isn't really (nat,), right for bonds?

Correct, fixed.

loriab · 2018-05-24T16:41:25Z

tests/input_failures/missing_molecule_symbols.json

@@ -1,6 +1,6 @@
 {
-    "schema_name": "QC_JSON",
-    "schema_version": 0,
+    "schema_name": "qc_json",


don't these have to be qc_schema or (qcschema, I'm confused)?

These are input failures and apparently not well enough tested. Fixed.

loriab · 2018-05-24T18:55:05Z

qcschema/dev/dev_schema.py

-    "name": "QC_JSON",
-    "version": "0.1.dev",
-    "url": "http://schema_host.org/schemas/0/something.schema",
+    "$schema": "http://json-schema.org/draft-04/schema#",


Ok, we'll just be on-guard for any field names involving id.

loriab · 2018-05-24T18:57:06Z

tests/output_failures/dipole_wrong_type.json

@@ -1,6 +1,6 @@
 {
-    "schema_name": "QC_JSON",
-    "schema_version": 0,
+    "schema_name": "qc_json",


needs renaming

loriab · 2018-05-24T18:57:19Z

tests/output_failures/unknown_property.json

@@ -1,6 +1,6 @@
 {
-    "schema_name": "QC_JSON",
-    "schema_version": 0,
+    "schema_name": "qc_json",


needs renaming

loriab · 2018-05-24T18:59:09Z

qcschema/dev/dev_schema.py

    "description": "The MolSSI Quantum Chemistry Schema",
    "type": "object",
    "properties": {
        "molecule": molecule.molecule,
        "schema_name": {
            "type": "string",
-            "pattern": "\W*(QC_JSON)\W*"
+            "pattern": "\W*(qc_schema)\W*"


Thanks for the distinction – makes much more sense now. (reference to docs was the sphinxproj name.)

loriab

lgtm

bennybp · 2018-06-04T20:23:54Z

lgtm, too. Don't think I have anything to add that would be required in v1.

Also, agree that separate/modular schema would be best and easier to manage.

dgasmith added 6 commits May 21, 2018 15:19

Moves qc_schema -> qcschema to be slightly more pythonic

271423e

Moves unimplemented features to a clear folder

dc6d64a

Changed schema_name to lowercase 'qc_schema' to properly reflect the …

0e817bb

…style conventions

Docs: Tech Specs -> Tech Discussion to reduce confusion

ef02225

Renames schema to qc_schema_*

7746f1c

Adds schema version structure and testing

891d506

loriab reviewed May 24, 2018

View reviewed changes

V1: Addresses name comments

a58854c

loriab reviewed May 24, 2018

View reviewed changes

loriab approved these changes May 24, 2018

View reviewed changes

Missed more qc_schema -> qc_schema_input fields

44eef21

bennybp merged commit 7669e5e into MolSSI:master Jun 5, 2018

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V1 release #49

V1 release #49

dgasmith commented May 22, 2018 •

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bennybp commented Jun 4, 2018

V1 release #49

V1 release #49

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dgasmith commented May 22, 2018 • edited Loading

Description

Questions

TODO

Status

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bennybp commented Jun 4, 2018

dgasmith commented May 22, 2018 •

edited

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