Prepare Publication (#38)

* Refractor (#26)

* update refractor

* fix reactor

* fix lint

* prepare bechmark

* refractor MODReactor and SynReactor

* update crn

* refractor cluster, change to matcher, fix code synreactor, now resnow comparable to modreactor

* test 3 os

* test

* test

* fix workflow

* fix lint

* fix win

* fix win

* fix win again

* update smart

* add synreactor implicit hydrogen

* fix mcsmatcher

* refractor visualization

* fix conflict rdkit, upgrade to 2025.3.1

* fix lint

* move aam_validator to Chem submodule

* fix lint

* prepare benchmark matcher

* change backend rule to mod

* prepare doc

* add doc

* update fih

* update graph module doc

* update doc

* prepare release

* .

* fix doc

* clean doc

* fix docstring

* fix tutorial

* update fig

* update explicit_hydrogen for its

* prepare release

* build doc

* fix lint

* fix bug in explicit hydrogen for ITS

* fix build

* fix

* fix

* fix

* fix doc

* update nauty canon, rule filters, change benchmark

* prepare release

* fix bug in nauty alg

* update doc

* add features for expanding its

* add rule_matcher.py

* add testcase rule matcher

* add wildcard for smiles

* add partial engine

* update new features

* update document

* add data

* update Chem features

* format docstring and refractor Chem module

* add auto-test pypi

* create dependabot

* test run yml

* test

* test docker

* add docker

* add docker

* .

* add readme

* rename

* release docker

* remove redundant file

* Prepare release bump version (#27)

* update refractor

* fix reactor

* fix lint

* prepare bechmark

* refractor MODReactor and SynReactor

* update crn

* refractor cluster, change to matcher, fix code synreactor, now resnow comparable to modreactor

* test 3 os

* test

* test

* fix workflow

* fix lint

* fix win

* fix win

* fix win again

* update smart

* add synreactor implicit hydrogen

* fix mcsmatcher

* refractor visualization

* fix conflict rdkit, upgrade to 2025.3.1

* fix lint

* move aam_validator to Chem submodule

* fix lint

* prepare benchmark matcher

* change backend rule to mod

* prepare doc

* add doc

* update fih

* update graph module doc

* update doc

* prepare release

* .

* fix doc

* clean doc

* fix docstring

* fix tutorial

* update fig

* update explicit_hydrogen for its

* prepare release

* build doc

* fix lint

* fix bug in explicit hydrogen for ITS

* fix build

* fix

* fix

* fix

* fix doc

* update nauty canon, rule filters, change benchmark

* prepare release

* fix bug in nauty alg

* update doc

* add features for expanding its

* add rule_matcher.py

* add testcase rule matcher

* add wildcard for smiles

* add partial engine

* update new features

* update document

* add data

* update Chem features

* format docstring and refractor Chem module

* add auto-test pypi

* create dependabot

* test run yml

* test

* test docker

* add docker

* add docker

* .

* add readme

* rename

* release docker

* remove redundant file

* fix lint

* fix bug

* fix lint

* add partial its beta

* test publising conda

* test publising conda

* fix workflow

* fix workflow

* fix workflow

* fix workflow again

* tes pre-release

* tes pre-release

* tes pre-release

* tes pre-release

* tes pre-release

* tes pre-release

* fix meta.yaml

* fix meta.yaml

* fix meta.yaml

* fix meta.yaml

* fix meta.yaml

* fix meta.yaml

* publish beta

* publish beta

* debug

* debug

* debug

* debug

* debug

* debug

* debug

* debug

* prepare release

* pass test staging, prepare release

* quick fix hydrogen

* prepare release

* Prepare release (#30)

* add partial its construction and imbaengine

* add wildcard and placeholder

* add testcase

* add mtg

* fix bug mtg

* prepare release

* Prepare release (#32)

* add partial its construction and imbaengine

* add wildcard and placeholder

* add testcase

* add mtg

* fix bug mtg

* prepare release

* enhance ITSConstruction to capture hydrogen

* add constraint for searching embedding

* fix hydro

* enhance batch reactor

* add postprocess

* fix cycle import and add data example

* fix package contain data

* fix bug release

* fix bug release

* Prepare Publication (#37)

* test context graph application and automorphism

* prepare for publication

* pass test, preparing for packaging

Author: TieuLongPhan

README.md

@@ -65,7 +65,7 @@ For more details on each utility within the repository, please refer to the docu
    ```bash
    docker pull tieulongphan/synkit:latest
    # or a specific version:
-   docker pull tieulongphan/synkit:0.1.0
+   docker pull tieulongphan/synkit:1.0.0
    ```
    Run a container (sanity check):
    ```

doc/conf.py

@@ -19,7 +19,7 @@
         release = m.version("synkit")
     except (ImportError, AttributeError):
         # Fallback default
-        release = "0.0.11"
+        release = "1.0.0"
 # Use only major.minor for short version
 version = ".".join(release.split(".")[:2])
 

lint.sh

@@ -29,6 +29,7 @@ reactor_engine.py,\
 groupoid.py,\
 syn_rule.py,\
 __init__.py,\
+topology.py,\
 dev/*,\
 Data \
   --statistics

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "0.0.17"
+version = "1.0.0"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 long-description = { file = "CHANGELOG.md" }

recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: synkit
-  version: "0.0.17"
+  version: "1.0.0"
 
 source:
   path: ..