Use new rydstate package

.github/workflows/generate_database.yml

@@ -12,50 +12,34 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        species: [Sr87, Sr88, Yb171, Yb173, Yb174]
+        species: [Sr87_mqdt, Sr88_mqdt, Yb171_mqdt, Yb173_mqdt, Yb174_mqdt]
         include:
-          # use n_max=220 for tags and main, but only n_max=110 for PRs, etc.
-          - n_max: ${{ (startsWith(github.ref, 'refs/tags/') || contains(github.ref, 'main')) && 220 || 110 }}
-          # for isotopes with hyperfine structure, we only include high-l states up to n=110 (otherwise the database size gets too large)
-          - species: Sr87
-            extra_args: "--n-max-high-l 110"
-          - species: Yb171
-            extra_args: "--n-max-high-l 110"
-          - species: Yb173
-            extra_args: "--n-max-high-l 110"
+          - extra_args: "--max-delta-nu 10 --all-nu-up-to 30"
+          # use nu-max=220 for tags and main, but only nu-max=100 for PRs, etc.
+          - arg_max: ${{ (startsWith(github.ref, 'refs/tags/') || github.ref == 'refs/heads/main') && '--nu-max 220' || '--nu-max 100' }}
     name: ${{ matrix.species }}
     runs-on: ubuntu-latest
     timeout-minutes: 300
-    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
-      actions: write
-      contents: read
     steps:
     - uses: actions/checkout@v6
       with:
         submodules: 'true'
-
-    - uses: julia-actions/setup-julia@v2
-      with:
-        version: 1.12
-        arch: x64
-    - uses: julia-actions/cache@v2
-
-    - name: Instantiate julia environment and link local MQDT.jl
-      run: julia --project=. -e 'import Pkg; Pkg.develop(path="MQDT.jl"); Pkg.instantiate()'
-
-    - name: Install and link local rydstate python package
-      run: julia --project=. -e 'using CondaPkg; CondaPkg.withenv() do; run(`python -m pip install -e rydstate`); end'
-
-    - name: Run generate_database
-      run: julia --project=. generate_database.jl ${{ matrix.species }} --directory database --n-max ${{ matrix.n_max }} ${{ matrix.extra_args }}
-
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Run generate_database.py
+      run: uv run py-spy record -o profile_${{ matrix.species }}.svg -- generate_database ${{ matrix.species }} --directory database/${{ matrix.species }}_v$(uv version --short) ${{ matrix.arg_max }} ${{ matrix.extra_args }}
     - name: Upload artifacts
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: database-${{ matrix.species }}
         path: |
           database/*/*.parquet
-
+    - name: Upload profile
+      if: always()
+      uses: actions/upload-artifact@v7
+      with:
+        name: profile-${{ matrix.species }}
+        path: profile*.svg
 
   github-release:
     name: Release database files to github releases
@@ -69,7 +53,7 @@ jobs:
 
     steps:
     - name: Download all the database files
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         path: database
         pattern: database-*
@@ -88,7 +72,7 @@ jobs:
         done
 
     - name: Release zipped database folders
-      uses: softprops/action-gh-release@v2
+      uses: softprops/action-gh-release@v3
       with:
         files: database/*.zip
         draft: true

.github/workflows/pre_commit.yml

@@ -15,17 +15,10 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1'
-      - uses: julia-actions/cache@v2
-      - name: Install JuliaFormatter
-        run: |
-          julia  -e 'import Pkg; Pkg.add("JuliaFormatter")'
       - uses: pre-commit/action@v3.0.1
       - run: git diff --output=format.patch --exit-code || { cat format.patch; false; }
         if: failure()
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         if: failure()
         with:
           name: format.patch

.gitignore

@@ -1,10 +1,18 @@
-# Ignore julia specific files
-Manifest*.toml
-.CondaPkg/
+# Ignore build and cache directories
+__pycache__/
+.ruff_cache/
+.mypy_cache/
+.venv/
+*.egg-info/
+wheelhouse/
+build/
+dist/
+.pytest_cache/
 
 # Ignore local development files
 playground/
 
 # Ignore the generated databases
 database/
 profiling/
+profiling*.svg

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "MQDT.jl"]
-	path = MQDT.jl
-	url = git@github.com:pairinteraction/MQDT.jl.git
-[submodule "rydstate"]
-	path = rydstate
+[submodule "RydState"]
+	path = RydState
 	url = git@github.com:pairinteraction/rydstate.git

.pre-commit-config.yaml

@@ -13,7 +13,15 @@ repos:
     hooks:
       - id: remove-tabs
 
-  - repo: "https://github.com/domluna/JuliaFormatter.jl"
-    rev: "v2.1.2"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
     hooks:
-      - id: "julia-formatter"
+      - id: ruff
+        args: ["--fix", "--exit-non-zero-on-fix"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.15.0
+    hooks:
+      - id: mypy
+        additional_dependencies: ["rydstate == 0.9"]

.python-version

@@ -0,0 +1 @@
+3.13.1

README.md

@@ -1,28 +1,27 @@
 # Tool for generating the MQDT database tables in the cloud
 
-Database of states and matrix elements calculated with multichannel quantum defect theory.
+Create the database including tables of states and matrix elements calculated with single-channel quantum defect theory.
 Database tables are available through [GitHub Releases](https://github.com/pairinteraction/database-mqdt/releases).
 
 ## Generate new tables locally
-To generate the database tables locally, first make sure you also downloaded MQDT.jl and rydstate as submodules (e.g. run `git submodule update --init`).
-
-Then, initialize the julia environment and link against the MQDT.jl package
-```bash
-julia --project=. -e 'import Pkg; Pkg.develop(path="MQDT.jl"); Pkg.instantiate()'
-```
-Also link against the python rydstate package via
-```bash
-julia --project=. -e 'using CondaPkg; CondaPkg.withenv() do; run(`python -m pip install -e rydstate`); end'
-```
-
-Finally, you can run the script to generate the tables via
+Run the script to generate the tables via
 ```bash
-julia --project=. generate_database.jl Yb174
+uv run generate_database <species_mqdt> --nu-max <nu-max> --directory <directory>
 ```
 
 ## Generate a new release
-To generate a new release with all the important tables, simply create and push a new annotated tag with a tag name of the form `v*.*` .
-This will run the `generate_database.yml` workflow, where first all tables are created (this happens for all commits, not only tags),
-and then in addition uploads the zipped versions of the tables to a new release with name `v*.*` .
+To generate a new release with all the important tables, simply create and push a new annotated tag with a tag name of the form `v*.*`.
+This will run the `generate_database.yml` workflow, where first all tables are created,
+and then in addition the zipped versions of the tables are uploaded to a new release with name `v*.*`.
 The release is created in draft mode, so you can double-check, that all database tables are included and optionally add a release text.
 Once you are happy with the release draft, don't forget to publish the release.
+
+## Misc
+
+### Profiling / Benchmarking
+To check the performance of this tool and to look for bottlenecks in the code, you can use [py-spy](https://github.com/benfred/py-spy) to profile the code.
+To do so simply run the following command:
+
+```bash
+uv run py-spy record -o profiling.svg -- generate_database <species_mqdt> --nu-max <nu-max>
+```