Pre-commit: Add markdown formatter

microsoft · Nov 27, 2023 · 3a879ef · 3a879ef
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,6 +22,12 @@ repos:
     args: [--autofix]
     exclude: tests/.*.yml
 
+- repo: https://github.com/executablebooks/mdformat
+  rev: 0.7.17
+  hooks:
+  - id: mdformat
+    args: [--wrap=120]
+
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.1.6
   hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,67 +3,100 @@
 ## `v0.4.1` - 2023-08-16
 
 ### Features
-- `PyscfCalculation`: Store serialized model as output [[a072ea6]](https://github.com/microsoft/aiida-pyscf/commit/a072ea6171b2204f94af8a6772a57fced0a0cef5)
-- `PyscfCalculation`: Add support for computing the Hessian [[05cefef]](https://github.com/microsoft/aiida-pyscf/commit/05cefefe5bac8ce59b59747c47f6e99d8f6abd37)
 
+- `PyscfCalculation`: Store serialized model as output
+  [(a072ea6)](https://github.com/microsoft/aiida-pyscf/commit/a072ea6171b2204f94af8a6772a57fced0a0cef5)
+- `PyscfCalculation`: Add support for computing the Hessian
+  [(05cefef)](https://github.com/microsoft/aiida-pyscf/commit/05cefefe5bac8ce59b59747c47f6e99d8f6abd37)
 
 ## `v0.4.0` - 2023-06-13
 
 ### Features
-- `PyscfCalculation`: Add support to compute charge density and MEP [[98445f4]](https://github.com/microsoft/aiida-pyscf/commit/98445f411a2a129d5e498299832fe4344b712551)
-- `PyscfCalculation`: Add the `trajectory` output [[78de8e0]](https://github.com/microsoft/aiida-pyscf/commit/78de8e033a5f11b7253b2208cec12a3edf23bf8f)
-- `PyscfBaseWorkChain`: Handle failed electronic convergence [[f138e71]](https://github.com/microsoft/aiida-pyscf/commit/f138e718b538460ae81f98cb5e7a038a907ad5c5)
-- `PyscfCalculation`: Add the `checkpoint` input [[d596f3d]](https://github.com/microsoft/aiida-pyscf/commit/d596f3dfae659c065e30c78673f4d24c2220cc1d)
-- `PyscfCalculation`: Add `checkpoint` file as output if not converged [[df15f83]](https://github.com/microsoft/aiida-pyscf/commit/df15f83553704470243bcc1da440557d9cc6155c)
-- `PyscfCalculation`: Add molecular orbital details to `parameters` output [[40eb22d]](https://github.com/microsoft/aiida-pyscf/commit/40eb22dba21eadf7dfe22ee0b02bb5c06082bc4a)
-- `PyscfCalculation`: Configure logging of geometric optimizer [[4308fca]](https://github.com/microsoft/aiida-pyscf/commit/4308fca2a1b6cb1e11baf273824a303a398e9504)
-- `PyscfCalculation`: Add `ERROR_IONIC_CONVERGENCE_NOT_REACHED` exit code [[711b7f8]](https://github.com/microsoft/aiida-pyscf/commit/711b7f8b5def5091519d66d4d3f79cba473096ac)
-- `PyscfBaseWorkChain`: Handle `ERROR_IONIC_CONVERGENCE_NOT_REACHED` [[7bb09f8]](https://github.com/microsoft/aiida-pyscf/commit/7bb09f8428c5ee753078a1c7822357d715f8cd17)
-- `PyscfBaseWorkChain`: Handle `ERROR_SCHEDULER_OUT_OF_WALLTIME` [[3075bfa]](https://github.com/microsoft/aiida-pyscf/commit/3075bfa0a3ee8cbecda380f9747bd6a7a90daff5)
-- `PyscfBaseWorkChain`: Handle `ERROR_SCHEDULER_NODE_FAILURE` [[6f494e7]](https://github.com/microsoft/aiida-pyscf/commit/6f494e761c1651f3c5efffaf564762ed0ddc4d0a)
+
+- `PyscfCalculation`: Add support to compute charge density and MEP
+  [(98445f4)](https://github.com/microsoft/aiida-pyscf/commit/98445f411a2a129d5e498299832fe4344b712551)
+- `PyscfCalculation`: Add the `trajectory` output
+  [(78de8e0)](https://github.com/microsoft/aiida-pyscf/commit/78de8e033a5f11b7253b2208cec12a3edf23bf8f)
+- `PyscfBaseWorkChain`: Handle failed electronic convergence
+  [(f138e71)](https://github.com/microsoft/aiida-pyscf/commit/f138e718b538460ae81f98cb5e7a038a907ad5c5)
+- `PyscfCalculation`: Add the `checkpoint` input
+  [(d596f3d)](https://github.com/microsoft/aiida-pyscf/commit/d596f3dfae659c065e30c78673f4d24c2220cc1d)
+- `PyscfCalculation`: Add `checkpoint` file as output if not converged
+  [(df15f83)](https://github.com/microsoft/aiida-pyscf/commit/df15f83553704470243bcc1da440557d9cc6155c)
+- `PyscfCalculation`: Add molecular orbital details to `parameters` output
+  [(40eb22d)](https://github.com/microsoft/aiida-pyscf/commit/40eb22dba21eadf7dfe22ee0b02bb5c06082bc4a)
+- `PyscfCalculation`: Configure logging of geometric optimizer
+  [(4308fca)](https://github.com/microsoft/aiida-pyscf/commit/4308fca2a1b6cb1e11baf273824a303a398e9504)
+- `PyscfCalculation`: Add `ERROR_IONIC_CONVERGENCE_NOT_REACHED` exit code
+  [(711b7f8)](https://github.com/microsoft/aiida-pyscf/commit/711b7f8b5def5091519d66d4d3f79cba473096ac)
+- `PyscfBaseWorkChain`: Handle `ERROR_IONIC_CONVERGENCE_NOT_REACHED`
+  [(7bb09f8)](https://github.com/microsoft/aiida-pyscf/commit/7bb09f8428c5ee753078a1c7822357d715f8cd17)
+- `PyscfBaseWorkChain`: Handle `ERROR_SCHEDULER_OUT_OF_WALLTIME`
+  [(3075bfa)](https://github.com/microsoft/aiida-pyscf/commit/3075bfa0a3ee8cbecda380f9747bd6a7a90daff5)
+- `PyscfBaseWorkChain`: Handle `ERROR_SCHEDULER_NODE_FAILURE`
+  [(6f494e7)](https://github.com/microsoft/aiida-pyscf/commit/6f494e761c1651f3c5efffaf564762ed0ddc4d0a)
 
 ### Changes
-- `PyscfCalculation`: Change filename format of FCIDUMP files [[5cd9094]](https://github.com/microsoft/aiida-pyscf/commit/5cd9094973edb63fe4fa6096ad224dcad6f5464f)
-- `PyscfCalculation`: Nest molecular orbitals in `cubegen` inputs/outputs [[68b204a]](https://github.com/microsoft/aiida-pyscf/commit/68b204a6102f51fea0c0334b16167273d9c0da3e)
-- `PyscfCalculation`: Improve the layout of the `parameters` output [[0145f2c]](https://github.com/microsoft/aiida-pyscf/commit/0145f2cd87b43f0fb4bdae330c633af5cb0586cd)
-- `PyscfCalculation`: Remove redirection of stderr to separate file [[90a7d07]](https://github.com/microsoft/aiida-pyscf/commit/90a7d07274fa97d9f43ff901fb3e198387b0f391)
-- `PyscfCalculation`: Remove the default `mean_field.method` [[6d223ad]](https://github.com/microsoft/aiida-pyscf/commit/6d223ada1e12a0027a717e93d5bc550605bade7d)
+
+- `PyscfCalculation`: Change filename format of FCIDUMP files
+  [(5cd9094)](https://github.com/microsoft/aiida-pyscf/commit/5cd9094973edb63fe4fa6096ad224dcad6f5464f)
+- `PyscfCalculation`: Nest molecular orbitals in `cubegen` inputs/outputs
+  [(68b204a)](https://github.com/microsoft/aiida-pyscf/commit/68b204a6102f51fea0c0334b16167273d9c0da3e)
+- `PyscfCalculation`: Improve the layout of the `parameters` output
+  [(0145f2c)](https://github.com/microsoft/aiida-pyscf/commit/0145f2cd87b43f0fb4bdae330c633af5cb0586cd)
+- `PyscfCalculation`: Remove redirection of stderr to separate file
+  [(90a7d07)](https://github.com/microsoft/aiida-pyscf/commit/90a7d07274fa97d9f43ff901fb3e198387b0f391)
+- `PyscfCalculation`: Remove the default `mean_field.method`
+  [(6d223ad)](https://github.com/microsoft/aiida-pyscf/commit/6d223ada1e12a0027a717e93d5bc550605bade7d)
 
 ### Fixes
-- `PyscfCalculation`: Fix bug in script if SCF does not converge [[03f03a0]](https://github.com/microsoft/aiida-pyscf/commit/03f03a002303ead896efe731bbd36240d4cbf3a8)
-- `PyscfParser`: Fix incorrect units of parsed optimized coordinates [[cfb5e5b]](https://github.com/microsoft/aiida-pyscf/commit/cfb5e5b7ff20d5685df9a214c682c88c2d7c79dc)
-- `PyscfParser`: Do not override scheduler exit code if set [[47dd59b]](https://github.com/microsoft/aiida-pyscf/commit/47dd59bf4d69c31d8ab777d62eafe7388a467506)
+
+- `PyscfCalculation`: Fix bug in script if SCF does not converge
+  [(03f03a0)](https://github.com/microsoft/aiida-pyscf/commit/03f03a002303ead896efe731bbd36240d4cbf3a8)
+- `PyscfParser`: Fix incorrect units of parsed optimized coordinates
+  [(cfb5e5b)](https://github.com/microsoft/aiida-pyscf/commit/cfb5e5b7ff20d5685df9a214c682c88c2d7c79dc)
+- `PyscfParser`: Do not override scheduler exit code if set
+  [(47dd59b)](https://github.com/microsoft/aiida-pyscf/commit/47dd59bf4d69c31d8ab777d62eafe7388a467506)
 
 ### Dependencies
-- Dependencies: Update requirement `mypy==1.3.0` [[631cf5f]](https://github.com/microsoft/aiida-pyscf/commit/631cf5f545a7d51b3a3afaa8e3c21cd9a561c5f1)
+
+- Dependencies: Update requirement `mypy==1.3.0`
+  [(631cf5f)](https://github.com/microsoft/aiida-pyscf/commit/631cf5f545a7d51b3a3afaa8e3c21cd9a561c5f1)
 
 ### Devops
-- `PyscfParser`: Add unit tests for parsing of FCIDUMP and CUBE files [[017757c]](https://github.com/microsoft/aiida-pyscf/commit/017757ceae3e99ca77d3ed4503c464350c16de6d)
 
+- `PyscfParser`: Add unit tests for parsing of FCIDUMP and CUBE files
+  [(017757c)](https://github.com/microsoft/aiida-pyscf/commit/017757ceae3e99ca77d3ed4503c464350c16de6d)
 
 ## `v0.3.0` - 2023-04-03
 
 ### Features
-- `PyscfCalculation`: Add support for writing FCIDUMP files [[#17]](https://github.com/microsoft/aiida-pyscf/pull/17)
-- `PyscfCalculation`: Add support for computing orbital cube files [[#20]](https://github.com/microsoft/aiida-pyscf/pull/20)
-- `PyscfCalculation`: Ensure strings are rendered with quotes in templates [[#19]](https://github.com/microsoft/aiida-pyscf/pull/19)
-- `PyscfCalculation`: Add validation for `optimizer` parameters [[#16]](https://github.com/microsoft/aiida-pyscf/pull/16)
-- `PyscfCalculation`: Refactor to simplify subclassing [[#22]](https://github.com/microsoft/aiida-pyscf/pull/22)
+
+- `PyscfCalculation`: Add support for writing FCIDUMP files [(#17)](https://github.com/microsoft/aiida-pyscf/pull/17)
+- `PyscfCalculation`: Add support for computing orbital cube files
+  [(#20)](https://github.com/microsoft/aiida-pyscf/pull/20)
+- `PyscfCalculation`: Ensure strings are rendered with quotes in templates
+  [(#19)](https://github.com/microsoft/aiida-pyscf/pull/19)
+- `PyscfCalculation`: Add validation for `optimizer` parameters
+  [(#16)](https://github.com/microsoft/aiida-pyscf/pull/16)
+- `PyscfCalculation`: Refactor to simplify subclassing [(#22)](https://github.com/microsoft/aiida-pyscf/pull/22)
 
 ### Documentation
-- Docs: Add setup and run instructions to `README.md` [[#18]](https://github.com/microsoft/aiida-pyscf/pull/18)
-- Docs: Add badges and table of contents to `README.md` [[#23]](https://github.com/microsoft/aiida-pyscf/pull/23)
+
+- Docs: Add setup and run instructions to `README.md` [(#18)](https://github.com/microsoft/aiida-pyscf/pull/18)
+- Docs: Add badges and table of contents to `README.md` [(#23)](https://github.com/microsoft/aiida-pyscf/pull/23)
 
 ### Devops
-- CI: Update `pip` and install `wheel` [[#21]](https://github.com/microsoft/aiida-pyscf/pull/21)
 
+- CI: Update `pip` and install `wheel` [(#21)](https://github.com/microsoft/aiida-pyscf/pull/21)
 
 ## `v0.2.0` - 2023-03-28
 
 ### Improvements
-- `PyscfCalculation`: Use `PrefixLoader` for template environment loader [[#12]](https://github.com/microsoft/aiida-pyscf/pull/12)
-- `PyscfCalculation`: Improve white-space in rendered script [[#13]](https://github.com/microsoft/aiida-pyscf/pull/13)
 
+- `PyscfCalculation`: Use `PrefixLoader` for template environment loader
+  [(#12)](https://github.com/microsoft/aiida-pyscf/pull/12)
+- `PyscfCalculation`: Improve white-space in rendered script [(#13)](https://github.com/microsoft/aiida-pyscf/pull/13)
 
 ## `v0.1.0` - 2023-03-27