Merge pull request #111 from siesta-project/Release1.2.0

Release1.2.0

Author: bosonie

.github/workflows/ci.yml

@@ -39,7 +39,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.6','3.7','3.8']
+        python-version: ['3.7','3.8',3.9]
 
     services:
         postgres:
@@ -75,7 +75,7 @@ jobs:
     - name: Install system dependencies
       run: |
         sudo apt update
-        sudo apt install postgresql-10
+        sudo apt install postgresql
     - name: Install python dependencies
       run: |
         pip install -e .[dev]

.github/workflows/develop.yml

@@ -8,13 +8,13 @@ jobs:
 
     tests:
 
-        if: github.repository == 'albgar/aiida_siesta_plugin'  # Prevent running the builds on forks as well
+        if: github.repository == 'siesta-project/aiida_siesta_plugin'  # Prevent running the builds on forks as well
 
         runs-on: ubuntu-latest
 
         strategy:
             matrix:
-                python-version: [3.6, 3.7, 3.8]
+                python-version: [3.7, 3.8, 3.9]
 
         services:
             postgres:
@@ -50,7 +50,7 @@ jobs:
         -   name: Install system dependencies
             run: |
                 sudo apt update
-                sudo apt install postgresql-10
+                sudo apt install postgresql
 
         -   name: Install python dependencies
             continue-on-error: true
@@ -66,16 +66,3 @@ jobs:
             id: tests
             run:
                 pytest -sv tests
-
-        -   name: Slack notification
-            if: steps.install.outcome == 'Failure' || steps.tests.outcome == 'Failure'
-            uses: rtCamp/action-slack-notify@master
-            env:
-                SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
-                SLACK_ICON: https://www.materialscloud.org/discover/images/0ba0a17d.aiida-logo-128.png
-                SLACK_USERNAME: aiida-siesta
-                SLACK_CHANNEL: actions
-                SLACK_COLOR: b60205
-                SLACK_TITLE: "Nightly build against `aiida-core/develop` failed"
-                SLACK_MESSAGE: "The tests fail with the current version of `aiida-core/develop`."
-

.pre-commit-config.yaml

@@ -9,12 +9,13 @@
         ^tests/
       )
 
-- repo: local
+
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.30.0
   hooks:
   - id: yapf
     name: yapf
     entry: yapf
-    language: system
     types: [python]
     args: ['-d']
     exclude:
@@ -23,6 +24,9 @@
         ^aiida_siesta/docs/|
         ^tests/
      )
+
+- repo: local
+  hooks:
   - id: prospector
     language: system
     types: [file, python]

.pylintrc

@@ -325,7 +325,8 @@ function-naming-style=snake_case
 # Good variable names which should always be accepted, separated by a comma
 good-names=i,x,
            j,y,
-           k,v,z,
+	   l,z,
+           k,v,
 	   qb,
            Run,
            UpfData,

CHANGELOG.md

@@ -1,5 +1,36 @@
 # Changelog
 
+## v1.2.0
+
+Version compatible with aiida-core>=1.3.0,<2.0.0.
+Support for python 3.6 has been dropped.
+
+### Improvements
+- Enable LUA interface to SIESTA. New inputs have been introduce to activate LUA control
+  over siesta calculations.
+- Access to the [sisl](https://github.com/zerothi/sisl) functionalities, since sisl is now
+  dependency of this package.
+- Introduction of the `IonData` data type that host the entity that in siesta terminology is called “ion”.
+  An "ion" packages the set of basis orbitals and KB projectors for a given species and therefore
+  can be use in substitution of the pseudo and basis inputs.
+  An `IonData` node is also returned in output for each species of the calculation so to help
+  the improve the tracking of used orbitals and KB projectors.
+  From an `IonData` instance, the list of orbitals of the calculation can be easily accessed in the form
+  of `SislAtomicOrbitals`.
+- Migration to the use of the [aiida-pseudo](https://github.com/aiidateam/aiida-pseudo) package for the
+  management of pseudo data types and families. The development on the the support for pseudopotentials
+  types has been centralized in an external package. The use of aiida-siesta custom classes `PsmlData`
+  and `PsfData` has been deprecated and will be remove in version 2.0.0.
+
+### Bug fixes
+- Fixed the atom heuristic selection of basis in the protocol system
+
+### For developers
+- Heavy refactoring to take advantage of the aiida-core validators system.
+- Start reorganization of folders. Especially moved the location of the protocols
+  system and of tkdict features.
+- Updated dependencies of tests and pre-commits.
+
 ## v1.1.1
 
 Version compatible with aiida-core>=1.3.0,<2.0.0.
@@ -30,7 +61,7 @@ Version compatible with aiida-core>=1.3.0,<2.0.0.
   and "kpoints" with value "None". This has been fixed.
   The method `inputs_generator().get_filled_builder` was instead correct.
 - A bug was leading to the failure of `SiestaSequentialConverger` in case one of
-  the parameters to coverge in the sequential process was not reacing convergence.
+  the parameters to converge in the sequential process was not reaching convergence.
   It is now fixed and, in addition, an output listing the unconverged parameters has been
   added.
 

MANIFEST.in

@@ -1,7 +1,12 @@
-include *.rst *.json *.txt *.md *.yml
-recursive-include aiida_siesta/docs/ *.rst
+include setup.json
+include AUTHORS.txt
+include CHANGELOG.md
+include PyPI-README.rst
+include LICENSE.txt
+graft aiida_siesta/examples/fixtures
 recursive-include aiida_siesta/examples/ *.txt *.psf *.psml *.cif 00_README
-recursive-include aiida_siesta/utils *.yaml
+include aiida_siesta/utils/protocols_system/*.yaml
+include aiida_siesta/utils/*.yaml
 prune tests
-prune aiida_siesta/docs/tutorialis/first_workchain
-prune aiida_siesta/docs/tutorialis/data_icn2_2020
+prune aiida_siesta/docs/tutorials/first_workchain
+prune aiida_siesta/docs/tutorials/data_icn2_2020

README.rst

@@ -18,8 +18,10 @@ This work is supported by the [MARVEL National Centre for Competency
 in Research](<http://nccr-marvel.ch>) funded by the `Swiss National
 Science Foundation <http://www.snf.ch/en>`_, as well as by the `MaX
 European Centre of Excellence <http://www.max-centre.eu/>`_ funded by
-the Horizon 2020 INFRAEDI-2018-1 program, Grant No. 824143, and by
-the Spanish MINECO (projects
+the Horizon 2020 INFRAEDI-2018-1 program, Grant No. 824143, by the
+`INTERSECT <https://intersect-project.eu/>`_  (Interoperable material-to-device simulation box for
+disruptive electronics) project, funded by Horizon 2020 under grant
+agreement No 814487, and by the Spanish MINECO (projects
 FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P)
 
 .. figure:: aiida_siesta/docs/miscellaneous/logos/MARVEL.png
@@ -30,6 +32,10 @@ FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P)
     :alt: MaX
     :target: http://www.max-centre.eu/
 
+.. figure:: aiida_siesta/docs/miscellaneous/logos/INTERSECT.png
+    :alt: INTERSECT
+    :target: http://intersect-project.eu/
+
 .. figure:: aiida_siesta/docs/miscellaneous/logos/MINECO-AEI.png
     :alt: MINECO-AEI
     :target: http://www.mineco.gob.es/

aiida_siesta/__init__.py

@@ -1,2 +1,2 @@
 """The official AiiDA plugin for Siesta."""
-__version__ = '1.1.1'
+__version__ = '1.2.0'