Big update (#24)

* update everything

* yet another NPM update?

* whatever, use another syntax

* remove library from github repository

* test upload lib

* try again using a tag

* build it or download it, but do not fetch it

* update to latest commit

* add LnPP2

* add test make library

* add BASIS_ZIJLSTRA

* update content

* add BASIS_ccGRB_UZH

.bumpversion.cfg

@@ -4,3 +4,4 @@ commit = True
 tag = True
 
 [bumpversion:file:cp2k_basis/__init__.py]
+[bumpversion:file:package.json]

.github/workflows/docs.yml

@@ -16,7 +16,6 @@ jobs:
           python-version: '3.10'
       - name: Install dependencies
         run: |
-          pip3 install pip-tools
           make install-dev
       - name: Build
         run: |

.github/workflows/publish-library.yml

@@ -0,0 +1,41 @@
+name: Publish library in (pre-)release
+
+on:
+  push:
+    branches: [ master, dev ]
+
+jobs:
+  build:
+    name: Make library
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          make install-dev
+      - name: Build
+        run: |
+           cb_fetch_data library/DATA_SOURCES.yml -o library.h5
+      - name: Upload pre-release version
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: library.h5
+          asset_name: latest_library.h5
+          tag: latest
+          overwrite: true
+          body: "Pre-release library"
+      - name: Upload release version
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: library.h5
+          asset_name: latest_library.h5
+          tag: ${{ github.ref }}
+          overwrite: true
+          body: "Stable release"

.github/workflows/tests.yml

@@ -1,7 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
+name: Run tests
 
 on:
   push:
@@ -15,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9, '3.10']
+        python-version: [3.9, '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2
@@ -28,7 +25,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip3 install pip-tools
         make install-dev
         make install-front
     - name: Lint
@@ -37,3 +33,6 @@ jobs:
     - name: Test
       run: |
         TEST_FETCH_DATA=1 make test
+    - name: Test make library
+      run: |
+        cb_fetch_data library/DATA_SOURCES.yml

.gitignore

@@ -255,4 +255,6 @@ cython_debug/
 
 node_modules/
 cp2k_basis_webservice/static
-tmp/
+tmp/
+library.h5
+latest_library.h5

Makefile

@@ -2,7 +2,7 @@ install:
 	pip install -e .
 
 install-dev:
-	pip-sync
+	pip install -e .[dev]
 
 install-front:
 	npm i

cp2k_basis/base_objects.py

@@ -205,7 +205,7 @@ def _read_metadata_hdf5(group: h5py.Group) -> dict:
         metadata = {}
 
         for key, values in group.attrs.items():
-            if type(values) == numpy.ndarray:
+            if type(values) is numpy.ndarray:
                 metadata[key] = list(values)
             else:
                 metadata[key] = values

cp2k_basis/parser.py

@@ -140,7 +140,7 @@ def integer(self) -> int:
         try:
             number = int(self.current_token.value)
         except ValueError:
-            raise ParserSyntaxError('expected integer, got {}'.format(self.current_token.value))
+            raise ParserSyntaxError('expected integer, got {}'.format(self.current_token))
 
         self.next()
         return number
@@ -153,7 +153,7 @@ def number(self) -> float:
         try:
             number = float(self.current_token.value)
         except ValueError:
-            raise ParserSyntaxError('expected number, got {}'.format(self.current_token.value))
+            raise ParserSyntaxError('expected number, got {}'.format(self.current_token))
 
         self.next()
         return number

cp2k_basis_webservice/__init__.py

@@ -40,7 +40,7 @@ class Config:
     API_LIMIT = '10/second'
 
     # library
-    LIBRARY = 'library/library.h5'
+    LIBRARY = 'instance/library.h5'
 
     # to be filled by `load_library()`
     BASIS_SETS_STORAGE = None

docs/developers/install.md

@@ -4,7 +4,7 @@
 
 First, install node. **It is recommended to use [`nvm`](https://github.com/nvm-sh/nvm#install--update-script) to do so.**
 
-Then:
+Then, install the project and its dependencies:
 
 ```bash
 # clone 
@@ -21,33 +21,30 @@ make install-front
 
 # build front
 make front
-
-# run the webservice:
-# either:
-make run
-# or,
-flask --app cp2k_basis_webservice run
 ```
 
-If you want to use your own library of basis and pseudopotentials, check out [this page](library_build.md), and then:
+Then, you can either build the library of basis sets and pseudopotentials, as described on [this page](library_build.md), or download its latest version (from the `dev` branch):
 
 ```bash
 # create an instance folder
 # see https://flask.palletsprojects.com/en/latest/config/#instance-folders
 mkdir instance
 
-# copy source
-cp library/DATA_SOURCES.yml instance/
-
-# after editing the DATA_SOURCES.yml file to fit your needs, 
-# run the `cb_fetch_data` command to create a new library:
-cb_fetch_data instance/DATA_SOURCES.yml -o instance/library.h5 
+# To download the library, use:
+wget https://github.com/pierre-24/cp2k-basis/releases/download/latest/latest_library.h5 -o instance/libary.h5
 
-# setup a custom config
-echo "LIBRARY='instance/library.h5'" > instance/settings.py
+# Alternatively, to build the library from scratch, use the `cb_fetch_data` command:
+cb_fetch_data library/DATA_SOURCES.yml -o instance/library.h5 
 ```
 
-And then you can restart the webservice.
+And finally, you can start the webservice:
+
+```bash
+# either:
+make run
+# or,
+flask --app cp2k_basis_webservice run
+```
 
 ## Contribute
 
@@ -75,10 +72,9 @@ make install-front
 
 ### Tips to contribute
 
-+ A useful setting is to setup the webservice to use the (smaller) test library for development:
++ A useful setting is to set up the webservice to use a (smaller) test library for development:
 
     ```bash
-    mkdir instance
     echo "LIBRARY='tests/LIBRARY_EXAMPLE.h5'" > instance/settings.py
     ```
 

docs/developers/library_build.md

@@ -16,7 +16,7 @@ From an existing YAML source file `DATA_SOURCE.yml` with the format described be
 cb_fetch_data DATA_SOURCES.yml -o library.h5
 ```
 
-This will create a [`library.h5` file](library_file_format.md), which might be exploited [latter on](#using-the-library).
+This will create a [`library.h5` file](library_file_format.md), which might be exploited [later on](#using-the-library).
 
 If you want to have insight on what is happening, you might want to use:
 
@@ -54,7 +54,7 @@ Keyword inside curly braces will be replaced by their value given in the `keywor
 
     the base URL will be `https://github.com/cp2k/cp2k/raw/786bc82ff9ded3e1f761cba6d8e25c3c9fe19bb1/data/`.
 
-Then, ach repository has different files (listed `files`).
+Then, each repository has different files (listed `files`).
 
 #### Files
 
@@ -166,7 +166,7 @@ The rules are the same as with `family_name`, but only the **first** result will
 Finaly, `cb_fetch_data`, it will add metadata to those families.
 
 To do so, the `metdata` dictionary will be used, in which the key is a REGEX matched against the name of the family.
-The if there is a match, then all the values are attributed as metadata.
+If there is a match, then all the values are attributed as metadata.
 
 ??? example
     With:
@@ -247,9 +247,6 @@ This file will follow the same syntax as the one described above [for files](#fi
 files:
 - name: BASIS_MOLOPT_UCL
   type: BASIS_SETS
-  family_name:
-  variant:
-metadata:
 ```
 
 You can now run `cb_explore_file` ... But nothing much happens:
@@ -281,7 +278,6 @@ Hopefully, the solution in this case is pretty straightforward: the name can be
         '^(.*)(-q\d{1,2})$': '\1'
       variant:
         '^.*-(q\d{1,2})$': '\1'
-    metadata:    
     ```
 
     The result is better: