diff --git a/.github/workflows/generate_database.yml b/.github/workflows/generate_database.yml
index 648591e..7d26f07 100644
--- a/.github/workflows/generate_database.yml
+++ b/.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
diff --git a/.github/workflows/pre_commit.yml b/.github/workflows/pre_commit.yml
index bd1bd47..2512b12 100644
--- a/.github/workflows/pre_commit.yml
+++ b/.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
diff --git a/.gitignore b/.gitignore
index 5fea1da..ec91ec7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,13 @@
-# 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/
@@ -8,3 +15,4 @@ playground/
 # Ignore the generated databases
 database/
 profiling/
+profiling*.svg
diff --git a/.gitmodules b/.gitmodules
index 8105a2a..e4fd816 100644
--- a/.gitmodules
+++ b/.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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6de0364..eac1dd9 100644
--- a/.pre-commit-config.yaml
+++ b/.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"]
diff --git a/.python-version b/.python-version
new file mode 100644
index 0000000..c10780c
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.13.1
diff --git a/CondaPkg.toml b/CondaPkg.toml
deleted file mode 100644
index 5844b45..0000000
--- a/CondaPkg.toml
+++ /dev/null
@@ -1,3 +0,0 @@
-[deps]
-python = ">=3.10, <3.14"
-pip = ">=23.0"
diff --git a/MQDT.jl b/MQDT.jl
deleted file mode 160000
index 2a9324d..0000000
--- a/MQDT.jl
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 2a9324d31589666740569cdad70d264d65a9bd54
diff --git a/Project.toml b/Project.toml
deleted file mode 100644
index 8a71a8c..0000000
--- a/Project.toml
+++ /dev/null
@@ -1,12 +0,0 @@
-[deps]
-ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
-CGcoefficient = "c862aa61-d51e-47d1-b396-b1e789b4e0b6"
-CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-LRUCache = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637"
-LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-MQDT = "1bfeae05-7215-4237-8fdd-b424babe7f02"
-OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-Parquet2 = "98572fba-bba0-415d-956f-fa77e587d26d"
-PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
diff --git a/README.md b/README.md
index dd4c735..5c95097 100644
--- a/README.md
+++ b/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>
+```
diff --git a/RydState b/RydState
new file mode 160000
index 0000000..dfeca00
--- /dev/null
+++ b/RydState
@@ -0,0 +1 @@
+Subproject commit dfeca005b672a28684fb438290529c39ed52ba30
diff --git a/angular.jl b/angular.jl
deleted file mode 100644
index 71fabca..0000000
--- a/angular.jl
+++ /dev/null
@@ -1,96 +0,0 @@
-using PythonCall
-using MQDT
-
-function calc_exp_qn(basisstate::BasisState, qn::String)
-    state = get_state(basisstate)
-    value = state.calc_exp_qn(qn)
-    return pyconvert(Float64, value)
-end
-
-function calc_exp_qn(basisarray::BasisArray, qn::String)
-    exp_list = Vector{Float64}(undef, size(basisarray))
-    for (i, state) in enumerate(basisarray.states)
-        exp_list[i] = calc_exp_qn(state, qn)
-    end
-    return exp_list
-end
-
-function calc_std_qn(basisstate::BasisState, qn::String)
-    state = get_state(basisstate)
-    value = state.calc_std_qn(qn)
-    return pyconvert(Float64, value)
-end
-
-function calc_std_qn(basisarray::BasisArray, qn::String)
-    std_list = Vector{Float64}(undef, size(basisarray))
-    for (i, state) in enumerate(basisarray.states)
-        std_list[i] = calc_std_qn(state, qn)
-    end
-    return std_list
-end
-
-function get_state(basisstate::BasisState)
-    rydstate = pyimport("rydstate")
-    channels = basisstate.channels.i
-    kets = Any[]
-    coeffs = Float64[]
-    coefficients = basisstate.coefficients[findall(basisstate.model.core)]
-    for (i, qn) in enumerate(channels)
-        # TODO how to handle channels with not well defined Jc or Fc
-        if isa(qn, jjQuantumNumbers) && isnan(qn.Jc)
-            continue
-        end
-        if isa(qn, fjQuantumNumbers) && (isnan(qn.Jc) || isnan(qn.Fc))
-            continue
-        end
-        push!(kets, get_ket(qn, basisstate.species))
-        push!(coeffs, coefficients[i])
-    end
-    state = rydstate.angular.AngularState(coeffs, kets; warn_if_not_normalized = false)
-    return state
-end
-
-function get_ket(qn::lsQuantumNumbers, species::Symbol)
-    rydstate = pyimport("rydstate")
-    ket = rydstate.angular.AngularKetLS(;
-        s_c = qn.sc,
-        s_tot = qn.S,
-        l_c = qn.lc,
-        l_r = qn.lr,
-        l_tot = qn.L,
-        j_tot = qn.J,
-        f_tot = qn.F,
-        species = String(species),
-    )
-    return ket
-end
-
-function get_ket(qn::jjQuantumNumbers, species::Symbol)
-    rydstate = pyimport("rydstate")
-    ket = rydstate.angular.AngularKetJJ(;
-        s_c = qn.sc,
-        l_c = qn.lc,
-        l_r = qn.lr,
-        j_c = qn.Jc,
-        j_r = qn.Jr,
-        j_tot = qn.J,
-        f_tot = qn.F,
-        species = String(species),
-    )
-    return ket
-end
-
-function get_ket(qn::fjQuantumNumbers, species::Symbol)
-    rydstate = pyimport("rydstate")
-    ket = rydstate.angular.AngularKetFJ(;
-        s_c = qn.sc,
-        l_c = qn.lc,
-        l_r = qn.lr,
-        j_c = qn.Jc,
-        f_c = qn.Fc,
-        j_r = qn.Jr,
-        f_tot = qn.F,
-        species = String(species),
-    )
-    return ket
-end
diff --git a/generate_database.jl b/generate_database.jl
deleted file mode 100644
index d38fd1e..0000000
--- a/generate_database.jl
+++ /dev/null
@@ -1,170 +0,0 @@
-using MQDT
-using CGcoefficient
-using Parquet2
-using ArgParse
-import Base.Filesystem: mkpath
-using DataFrames
-using OrderedCollections
-using Logging, LoggingExtras
-using LRUCache
-
-
-include("utils.jl")
-HIGH_L = 10
-
-version = "v1.2"
-
-function parse_commandline()
-    s = ArgParseSettings(
-        description = "Generate a database, containing energies and matrix elements, for a given species.",
-        epilog = "Example:\n  julia --project=. generate_database.jl Yb174",
-    )
-
-    @add_arg_table! s begin
-        "species"
-        help = "The species to generate the database for"
-        required = true
-        arg_type = String
-        "--n-min-sqdt"
-        help = "The minimal principal quantum number n for the SQDT models to be included in the database."
-        default = 25
-        arg_type = Int
-        "--n-max-high-l"
-        help = "The maximal principal quantum number n for high angular momentum states (l > $HIGH_L) to be included in the database."
-        default = Inf
-        arg_type = Float64
-        "--n-max"
-        help = "The maximum principal quantum number n for the states to be included in the database."
-        default = 110
-        arg_type = Int
-        "--directory"
-        help = "The directory where the database will be saved"
-        default = "database"
-        arg_type = String
-        "--overwrite"
-        help = "Delete the species folder if it exists and create a new one"
-        action = :store_true
-    end
-
-    return parse_args(s)
-end
-
-
-function main()
-    # Parse command line arguments
-    args = parse_commandline()
-    n_max = args["n-max"]
-    n_min_sqdt = args["n-min-sqdt"]
-    n_max_high_l = args["n-max-high-l"]
-    directory = args["directory"]
-    overwrite = args["overwrite"]
-    species = Symbol(args["species"])
-
-    # Setup output directory
-    output_dir = "$(directory)/$(species)_mqdt_$(version)"
-    if overwrite
-        rm(output_dir, recursive = true, force = true)
-    elseif isdir(output_dir)
-        error("Output directory already exists: $output_dir. Use --overwrite to overwrite.")
-    end
-    mkpath(output_dir)
-
-    # Setup logging to both file and console
-    console_logger = ConsoleLogger(stdout)
-    file_logger = SimpleLogger(open("$(output_dir)/$(species).log", "w"))
-    combined_logger = TeeLogger(console_logger, file_logger)
-    global_logger(combined_logger)
-
-    @info "Starting database generation for $species with version $version"
-    @info "Parameters: $args"
-    start_time = time()
-
-    # initialize Wigner symbol calculation
-    CGcoefficient.wigner_init_float(n_max - 1, "Jmax", 9)
-
-    parameters = MQDT.get_species_parameters(species)
-    all_models = Vector{MQDT.fModel}()
-
-    s_r = 1 / 2
-    j_c = 1 / 2
-    i_c = parameters.spin
-    seen_models = Set{String}()
-    for l_r = 0:(n_max-1)
-        for j_r = abs(l_r-s_r):1:(l_r+s_r)
-            for f_c = abs(j_c-i_c):1:(j_c+i_c)
-                for f_tot = abs(f_c-j_r):1:(f_c+j_r)
-                    models = MQDT.get_fmodels(species, l_r, j_r, f_c, f_tot, parameters)
-                    for model in models
-                        if !(model.name in seen_models)
-                            push!(seen_models, model.name)
-                            push!(all_models, model)
-                        end
-                    end
-                end
-            end
-        end
-    end
-
-    @info "Calculating MQDT states..."
-    states = Vector{MQDT.EigenStates}(undef, length(all_models))
-    for (i, M) in enumerate(all_models)
-        _n_min = NaN
-        _n_max = n_max
-        if startswith(M.name, "SQDT")
-            _n_min = n_min_sqdt
-            if parameters.spin > 0
-                l_ryd = MQDT.get_lr(M)[1]
-                if l_ryd >= n_max_high_l
-                    _n_max = 0
-                elseif l_ryd > HIGH_L
-                    _n_max = min(n_max_high_l, n_max)
-                end
-            end
-        end
-        @info "$(M.name)"
-        states[i] = MQDT.eigenstates(_n_min, _n_max, M, parameters)
-        if length(states[i].n) > 0
-            @info "  found nu_min=$(minimum(states[i].n)), nu_max=$(maximum(states[i].n)), total states=$(length(states[i].n))"
-        else
-            @info "  found no states"
-        end
-    end
-
-    basis = MQDT.basisarray(states, all_models)
-    @info "Generated state table with $(length(basis.states)) states"
-
-    @info "Converting states to database table..."
-    @timelog states_df = basis_to_df(basis, parameters)
-
-    @info "Calculating matrix elements..."
-    @timelog row_col_value_dict = all_matrix_element(basis, parameters)
-
-    @info "Converting matrix elements to database table..."
-    @timelog matrix_elements_df_dict =
-        Dict(k => rcv_to_df(v) for (k, v) in row_col_value_dict)
-
-    @info "Storing database tables as parquet files..."
-    tables = merge(Dict("states" => states_df), matrix_elements_df_dict)
-    for (name, table) in tables
-        @info "$(name) info" rows=nrow(table)
-        @info describe(table)
-        @timelog Parquet2.writefile("$(output_dir)/$(name).parquet", table)
-    end
-
-    elapsed_time = round(time() - start_time, digits = 2)
-    @info "Database generation completed" elapsed_seconds=elapsed_time
-    @info "Output saved to: $output_dir"
-
-    @info "Cache information MQDT.lru_radial_moment:"
-    @info cache_info(MQDT.lru_radial_moment)
-    @info "Cache information MQDT.lru_get_rydberg_state:"
-    @info cache_info(MQDT.lru_get_rydberg_state)
-    @info "Cache information MQDT.lru_angular_matrix:"
-    @info cache_info(MQDT.lru_angular_matrix)
-    @info "Cache information MQDT.lru_magnetic_matrix:"
-    @info cache_info(MQDT.lru_magnetic_matrix)
-
-end
-
-
-main()
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..f7792e6
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,20 @@
+[project]
+name = "database-mqdt"
+version = "1.2"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE.txt"]
+requires-python = ">=3.10"
+dependencies = ["rydstate >= 0.10"]
+
+
+[tool.uv.sources]
+rydstate = { path = "RydState", editable = true }
+
+
+[dependency-groups]
+dev = [
+  "pip",
+  "ipykernel",
+  "py-spy",
+]
diff --git a/rydstate b/rydstate
deleted file mode 160000
index 2095748..0000000
--- a/rydstate
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 2095748c6faa61a9221f375a24d52a14901c9630
diff --git a/tools/compare/.gitignore b/tools/compare/.gitignore
new file mode 100644
index 0000000..10a3cd3
--- /dev/null
+++ b/tools/compare/.gitignore
@@ -0,0 +1,18 @@
+# Ignore build and cache directories
+__pycache__/
+.ruff_cache/
+.mypy_cache/
+.venv/
+.pytest_cache/
+
+# Ignore local development files
+playground/
+
+# Ignore uv lock
+uv.lock
+
+# Ignore the database and log files
+*.parquet
+*.db-journal
+*.db
+log
diff --git a/tools/compare/README.md b/tools/compare/README.md
new file mode 100644
index 0000000..105fa80
--- /dev/null
+++ b/tools/compare/README.md
@@ -0,0 +1,9 @@
+This is a collection of simple scripts to compare old to new databases (for states, matrix elements and wigner tables).
+This can be helpful to see, if and what changed from a previous version to a newer version of the database files.
+
+# Run the compare script
+First copy a new and an old version of the databases inside this folder (e.g. "Rb_v1.0/" and "Rb_v1.1/")
+and adapt the `new_path` and `old_path` variables inside the corresponding `compare_....py` script.
+Now, you can run `uv run compare_....py`.
+
+Optionally, you can adjust some of the arguments to the compare functions (e.g. the relative (rtol) and absolute (atol) tolerances) to your needs.
diff --git a/tools/compare/compare_matrix_elements.py b/tools/compare/compare_matrix_elements.py
new file mode 100644
index 0000000..af4aae2
--- /dev/null
+++ b/tools/compare/compare_matrix_elements.py
@@ -0,0 +1,138 @@
+from pathlib import Path
+
+import pandas as pd
+
+from utils import add_global_uid_column
+
+TABLE_NAMES: list[str] = [
+    "matrix_elements_d",
+    "matrix_elements_q",
+    "matrix_elements_o",
+    "matrix_elements_q0",
+    "matrix_elements_mu",
+]
+
+
+def main() -> None:
+    # CHANGE THESE PATHS, TO THE FOLDERS YOU WANT TO COMPARE
+    db_dir = Path(__file__).parent.parent.parent / "database"
+    species = "Yb174_mqdt"
+    old_path = db_dir / f"{species}_v1.2"
+    new_path = db_dir / f"{species}_v1.3"
+
+    print(f"Comparing matrix elements tables:\n  New: {new_path}\n  Old: {old_path}")
+    for table_name in TABLE_NAMES:
+        if not (new_path / f"{table_name}.parquet").exists() or not (old_path / f"{table_name}.parquet").exists():
+            print(f"\nSkipping {table_name} as it does not exist in either the new or the old path.\n")
+            continue
+        compare_matrix_elements_table(table_name, new_path, old_path)
+
+
+def compare_matrix_elements_table(  # noqa: C901, PLR0915
+    table_name: str,
+    new_path: Path,
+    old_path: Path,
+    rtol: float = 1e-2,
+    atol: float = 1e-5,
+    *,
+    min_nu: float = 0,
+    max_nu: float = float("inf"),
+    max_delta_nu: int = 3,
+    only_compare_absolute_values: bool = False,
+    verbose: bool = False,
+) -> None:
+    """Compare the matrix elements table of two versions of the database.
+
+    Given the path to states and matrix elements parquet tables,
+    this function will
+    1) create a new index mapping from a state (defined by n, exp_l, and exp_j) to a unique identifier
+    2) replace the old id_initial and id_final column in the matrix elements table with this new index
+    3) compare the column "val" of the two matrix elements tables.
+
+    """
+    print(f"Comparing matrix elements table:     {table_name}")
+
+    species = new_path.name.split("_v")[0]
+    if species != old_path.name.split("_v")[0]:
+        raise ValueError(f"Cannot compare different species: {species} vs {old_path.name.split('_v')[0]}")
+
+    paths = {"new": new_path, "old": old_path}
+    states_dict = {key: pd.read_parquet(path / "states.parquet") for key, path in paths.items()}
+    table_dict = {key: pd.read_parquet(path / f"{table_name}.parquet") for key, path in paths.items()}
+    print(f"  Table shape pre-filtering:    New: {table_dict['new'].shape}; Old: {table_dict['old'].shape}")
+
+    all_columns = ["id_initial", "id_final", "val"]
+    for key, table in table_dict.items():
+        missing_cols = [col for col in all_columns if col not in table.columns]
+        if len(missing_cols) > 0:
+            print(f"WARNING: {key.capitalize()} table is missing columns: {missing_cols}")
+        extra_cols = [col for col in table.columns if col not in all_columns and col != "id"]
+        if len(extra_cols) > 0:
+            print(f"WARNING: {key.capitalize()} table has extra columns: {extra_cols}")
+
+    # Filter states and matrix elements tables by nu and delta_nu
+    for key, states in states_dict.items():
+        add_global_uid_column(species, states)
+        id_to_global_uid = dict(zip(states["id"], states["global_uid"], strict=True))
+
+        # Add columns global_uid_initial and global_uid_final to the matrix elements table
+        table = table_dict[key]
+        for which in ["initial", "final"]:
+            table[f"global_uid_{which}"] = table[f"id_{which}"].map(id_to_global_uid)
+            if table[f"global_uid_{which}"].isna().any():  # this should not happen
+                raise ValueError(f"Some {which} ids in {key} table dont have a entry in the states table.")
+
+        # Set new column nu_... and filter by it
+        id_to_nu = dict(zip(states["id"], states["nu"], strict=True))
+        for which in ["initial", "final"]:
+            table[f"nu_{which}"] = table[f"id_{which}"].map(id_to_nu)
+            table_dict[key] = table = table[table[f"nu_{which}"] >= min_nu].copy()
+            table_dict[key] = table = table[table[f"nu_{which}"] <= max_nu].copy()
+
+        # Set new column with delta_nu = abs(nu_final - nu_initial) and filter by it
+        table["delta_nu"] = (table["nu_final"] - table["nu_initial"]).abs()
+        table_dict[key] = table = table[table["delta_nu"] <= max_delta_nu].copy()
+
+        # Index the matrix elements by the global state uid pair
+        table = table.set_index(["global_uid_initial", "global_uid_final"], drop=False)
+        table_dict[key] = table.sort_index()
+    print(f"  Table shape after-filtering:  New: {table_dict['new'].shape}; Old: {table_dict['old'].shape}")
+
+    # Only keep entries that are present in both tables
+    new, old = table_dict["new"], table_dict["old"]
+    common_index = new.index.intersection(old.index)
+    for table in table_dict.values():
+        table.drop(index=common_index.symmetric_difference(table.index), inplace=True, errors="ignore")  # noqa: PD002
+        table.sort_index(inplace=True)  # noqa: PD002
+    print(f"  Common entries: {new.shape[0]}")
+
+    # Compare val values within tolerance
+    val_str = "val"
+    if only_compare_absolute_values:
+        new["val"] = new["val"].abs()
+        old["val"] = old["val"].abs()
+        val_str = "|val|"
+
+    val_diff = (new["val"] - old["val"]).abs()
+    tolerance = atol + rtol * old["val"].abs()
+    val_mask = val_diff.gt(tolerance)
+
+    print(f"  Found {val_mask.sum()}/{val_mask.shape[0]} differences outside tolerance:")
+    if verbose and val_mask.any():
+        diff_uids = val_mask.loc[val_mask].index
+        for uid in diff_uids:
+            new_val = new.loc[uid, "val"]
+            old_val = old.loc[uid, "val"]
+            diff_val = val_diff.loc[uid]
+            print(f"    State initial: {uid[0]}, State final: {uid[1]}")
+            print(f"      New {val_str}: {new_val:.5f}, Old {val_str}: {old_val:.5f}")
+            print(f"      Absolute difference: {diff_val:.2e}, Relative difference: {diff_val / abs(old_val):.2e}")
+
+    rdiff = val_diff / old["val"].abs()
+    print(f"  Maximum absolute {val_str} difference: {val_diff.max():.2e}")
+    print(f"  Maximum relative {val_str} difference: {rdiff.max():.2e}")
+    print()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tools/compare/compare_states.py b/tools/compare/compare_states.py
new file mode 100644
index 0000000..e5b7ff5
--- /dev/null
+++ b/tools/compare/compare_states.py
@@ -0,0 +1,173 @@
+from pathlib import Path
+from typing import Literal
+
+import pandas as pd
+
+from utils import add_global_uid_column
+
+COLUMNS_COMPARE_EXACT = ["id", "n", "f", "is_j_total_momentum", "is_calculated_with_mqdt", "parity"]
+COLUMNS_COMPARE_NUMERICAL = [
+    "energy",
+    "nu",
+    "exp_nui",
+    "std_nui",
+    "exp_l",
+    "std_l",
+    "exp_j",
+    "std_j",
+    "exp_s",
+    "std_s",
+    "exp_l_ryd",
+    "std_l_ryd",
+    "exp_j_ryd",
+    "std_j_ryd",
+    "underspecified_channel_contribution",
+]
+VERBOSE_COLUMNS: list[str] = []
+
+
+def main() -> None:
+    # CHANGE THESE PATHS, TO THE FOLDERS YOU WANT TO COMPARE
+    db_dir = Path(__file__).parent.parent.parent / "database"
+    species = "Yb174_mqdt"
+    old_path = db_dir / f"{species}_v1.2"
+    new_path = db_dir / f"{species}_v1.3"
+
+    compare_states_table(new_path, old_path, compare_id=False, verbosity="none")
+
+
+def compare_states_table(  # noqa: C901, PLR0912, PLR0915
+    new_path: Path,
+    old_path: Path,
+    rtol: float = 1e-8,
+    atol: float = 1e-10,
+    *,
+    min_nu: float = 0,
+    max_nu: float = float("inf"),
+    compare_id: bool = False,
+    verbosity: Literal["none", "all", "diff", "states"],
+) -> None:
+    """Compare the states table of two versions of the database.
+
+    Given two parquet files containing the states table, with the following columns:
+    - n: principal quantum number
+    - exp_l: experimental orbital angular momentum
+    - exp_j: experimental total angular momentum
+    - energy: energy of the state
+    - etc.
+    This function will compare the tables by
+    i) checking if both tables include the same states (a state is defined by the combination of n, exp_l, and exp_j)
+    ii) checking if the energy values of the states are equal within a given tolerance (rtol and atol).
+    iii) checking if all other columns are exactly equal.
+
+    """
+    print(f"Comparing states tables:\n  New: {new_path}\n  Old: {old_path}\n")
+
+    species = new_path.name.split("_v")[0]
+    if species != old_path.name.split("_v")[0]:
+        raise ValueError(f"Cannot compare different species: {species} vs {old_path.name.split('_v')[0]}")
+
+    paths = {"new": new_path, "old": old_path}
+    states_dict = {key: pd.read_parquet(path / "states.parquet") for key, path in paths.items()}
+
+    for key, states in states_dict.items():
+        print(f"{key.capitalize()} states table:")
+        shape_pre = states.shape
+        states_dict[key] = states[(states["nu"] >= min_nu) & (states["nu"] <= max_nu)]
+        print(f"  Table shape: Pre-filtering: {shape_pre}; After-filtering: {states.shape}")
+        print()
+
+    all_columns = COLUMNS_COMPARE_EXACT + COLUMNS_COMPARE_NUMERICAL
+    for key, states in states_dict.items():
+        missing_cols = [col for col in all_columns if col not in states.columns]
+        if len(missing_cols) > 0:
+            print(f"WARNING: {key.capitalize()} states table is missing columns: {missing_cols}")
+        extra_cols = [col for col in states.columns if col not in all_columns and col != "id"]
+        if len(extra_cols) > 0:
+            print(f"WARNING: {key.capitalize()} states table has extra columns: {extra_cols}")
+
+    for states in states_dict.values():
+        add_global_uid_column(species, states)
+
+    # Check if both tables have the same states
+    only_in_new = set(states_dict["new"].index) - set(states_dict["old"].index)
+    only_in_old = set(states_dict["old"].index) - set(states_dict["new"].index)
+
+    if only_in_new or only_in_old:
+        print("States don't match between tables:")
+        if only_in_new:
+            print(f"  {len(only_in_new)} states only in new table:")
+            if verbosity in ["all", "states"]:
+                for state in sorted(only_in_new):
+                    print(f"  State({state})")
+        if only_in_old:
+            print(f"  {len(only_in_old)} states only in old table:")
+            if verbosity in ["all", "states"]:
+                for state in sorted(only_in_old):
+                    print(f"  State({state})")
+
+        # Remove non-matching states from both tables
+        states_dict["new"] = states_dict["new"].drop(index=list(only_in_new), errors="ignore")
+        states_dict["old"] = states_dict["old"].drop(index=list(only_in_old), errors="ignore")
+
+    if len(states_dict["new"]) == 0:
+        raise ValueError("No matching states to compare.")
+    if len(states_dict["new"]) != len(states_dict["old"]):
+        raise ValueError("This should not happen: After filtering, both tables should have the same number of states.")
+    print(f"Continuing comparison with {len(states_dict['new'])} matching states ...\n")
+
+    columns_without_diff: list[str] = []
+    new, old = states_dict["new"], states_dict["old"]
+
+    # Compare all columns that should be exactly equal
+    for col in COLUMNS_COMPARE_EXACT:
+        if not compare_id and col == "id":
+            continue
+
+        differences = new[col].ne(old[col])
+        if not differences.any():
+            columns_without_diff.append(col)
+            continue
+
+        print(f"Found {differences.sum()} differences in column '{col}':")
+        if verbosity in ["all", "diff"] or col in VERBOSE_COLUMNS:
+            diff_states = differences.loc[differences].index
+            for state in diff_states:
+                print(f"  State({state})")
+                print(f"    New value: {new.loc[state, col]}")
+                print(f"    Old value: {old.loc[state, col]}")
+    print()
+
+    # Compare numeric values within tolerance
+    for col in COLUMNS_COMPARE_NUMERICAL:
+        differences = (new[col] - old[col]).abs()
+        tolerance = atol + rtol * old[col].abs()
+        mask = differences.gt(tolerance)
+
+        if mask.sum() == 0 and differences.max() < 1e-15:  # noqa: PLR2004
+            columns_without_diff.append(col)
+            continue
+
+        print(f"Found {mask.sum()} {col} differences outside tolerance:")
+        if (verbosity in ["all", "diff"] and mask.any()) or col in VERBOSE_COLUMNS:
+            diff_states = mask.loc[mask].index
+            for state in diff_states:
+                new_val = new.loc[state, col]
+                old_val = old.loc[state, col]
+                diff = differences.loc[state]
+                print(f"  State({state}):")
+                print(f"    New {col}: {new_val:.12f}")
+                print(f"    Old {col}: {old_val:.12f}")
+                print(f"    Absolute difference: {diff:.2e}")
+                print(f"    Relative difference: {diff / abs(old_val):.2e}")
+
+        max_rdiff = (differences / old[col].abs()).max()
+        print(f"  Maximum absolute {col} difference: {differences.max():.2e}")
+        print(f"  Maximum relative {col} difference: {max_rdiff:.2e}")
+    print()
+
+    print(f"Columns without differences: {', '.join(columns_without_diff)}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tools/compare/pyproject.toml b/tools/compare/pyproject.toml
new file mode 100644
index 0000000..5e29b10
--- /dev/null
+++ b/tools/compare/pyproject.toml
@@ -0,0 +1,34 @@
+[project]
+name = "compare-databases"
+version = "0.2.0"
+description = "Compare databases produced by the RydState package."
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+  "pandas[pyarrow] >= 2.2.3",
+]
+
+
+[tool.ruff]
+line-length = 120
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["ALL"]
+extend-ignore = [
+  "PLR0913",  # Too many arguments in function definition (... > 5)
+  "D1",  # remove once more docstrings are added
+  "TRY003",  # Avoid specifying long messages outside the exception class
+  "EM",  # Exceptions ...
+  "COM812",  # (missing-trailing-comma) incompatible with ruff format
+  "D203",  # (incorrect-blank-line-before-class) incompatible with D211: no-blank-line-before-class
+  "D213",  # (multi-line-summary-second-line) incompatible with D212: multi-line-summary-first-line
+  "T201",  # allow print
+  "INP001",  # no package
+]
+
+
+[tool.mypy]
+strict = true
+disallow_untyped_decorators = false
+ignore_missing_imports = true
diff --git a/tools/compare/utils.py b/tools/compare/utils.py
new file mode 100644
index 0000000..a405c3c
--- /dev/null
+++ b/tools/compare/utils.py
@@ -0,0 +1,52 @@
+import pandas as pd
+
+SQDT_INDEX_COLUMNS: dict[str, int | None] = {
+    "n": None,
+    "exp_l": None,
+    "exp_j": None,
+    "exp_s": None,
+}
+MQDT_INDEX_COLUMNS: dict[str, int | None] = {
+    "nu": 2,
+    "f": None,
+    "exp_l": 1,
+    "exp_j": 1,
+    "exp_j_ryd": 1,
+}
+
+
+def add_global_uid_column(species: str, states: pd.DataFrame) -> None:
+    """Return a copy of the states table indexed by a database-independent state key."""
+    index_columns = get_index_columns(species)
+    missing_columns = [col for col in index_columns if col not in states.columns]
+    if missing_columns:
+        raise ValueError(f"States table is missing index columns: {missing_columns}")
+
+    states_copy = states.copy()
+    for col, decimals in index_columns.items():
+        if decimals is not None:
+            states_copy[col] = states_copy[col].round(decimals)
+    if "mqdt" in species:
+        states_copy["exp_j_ryd"] = (2 * states_copy["exp_j_ryd"]).round(0) / 2
+
+    global_uid = [
+        ", ".join(f"{col}={state[i]}" for i, col in enumerate(index_columns))
+        for state in states_copy[list(index_columns)].itertuples(index=False, name=None)
+    ]
+    global_index = pd.Index(global_uid, name="global_uid")
+    if not global_index.is_unique:
+        duplicate_descriptions = list(global_index[global_index.duplicated(keep=False)].drop_duplicates())[:5]
+        details = "; ".join(duplicate_descriptions)
+        if global_index.duplicated(keep=False).sum() > len(duplicate_descriptions):
+            details += "; ..."
+        raise ValueError(f"Duplicate global state index: {details}")
+
+    states["global_uid"] = global_uid
+    states.index = global_index
+
+
+def get_index_columns(species: str) -> dict[str, int | None]:
+    """Return the index columns for a given species."""
+    if "mqdt" in species:
+        return MQDT_INDEX_COLUMNS
+    return SQDT_INDEX_COLUMNS
diff --git a/utils.jl b/utils.jl
deleted file mode 100644
index d98848d..0000000
--- a/utils.jl
+++ /dev/null
@@ -1,228 +0,0 @@
-import LinearAlgebra
-import MQDT
-include("angular.jl")
-
-
-const START_ID = 0
-
-macro timelog(expr)
-    quote
-        local result, elapsed_time, bytes_allocated, gc_time, memory_counters =
-            @timed $(esc(expr))
-        @info "$(round(elapsed_time, digits=6)) seconds (allocations: $(Base.format_bytes(bytes_allocated)), $(round(100 * gc_time / elapsed_time, digits=2))% gc time)"
-        result
-    end
-end
-
-
-function get_relevant_lr(state::MQDT.BasisState)
-    inds = findall(state.model.core)
-    return state.lr_list[inds]
-end
-
-function get_relevant_nu(state::MQDT.BasisState)
-    inds = findall(state.model.core)
-    return state.nu_list[inds]
-end
-
-function all_matrix_element(B::MQDT.BasisArray, parameters::MQDT.Parameters)
-    """Calculate all relevant matrix elements for a given basis array B.
-
-    This means dipole, quadrupole, magnetic, and diamagnetic matrix elements.
-    """
-    k_angular_max = 2  # 2 for now, since we dont calculate octupole matrix elements
-
-    row_col_value = Dict(
-        "matrix_elements_d" => Tuple{Int64,Int64,Float64}[],
-        "matrix_elements_q" => Tuple{Int64,Int64,Float64}[],
-        "matrix_elements_mu" => Tuple{Int64,Int64,Float64}[],
-        "matrix_elements_q0" => Tuple{Int64,Int64,Float64}[],
-    )
-
-    states_indexed = [(ids, state) for (ids, state) in enumerate(B.states)]
-    states_lr = [get_relevant_lr(s) for (_, s) in states_indexed]
-    states_nu = [get_relevant_nu(s) for (_, s) in states_indexed]
-
-    states_sorted = sort(
-        states_indexed,
-        by = x ->
-            (minimum(get_relevant_lr(x[2])), minimum(get_relevant_nu(x[2])), x[1]),
-    )
-
-    for (i1, (id1, s1)) in enumerate(states_sorted)
-        lr1 = states_lr[id1]
-        nus1 = states_nu[id1]
-        for (id2, s2) in states_sorted[i1:end]
-            lr2 = states_lr[id2]
-            # Skip if all contributions of the two states are far apart in angular momentum
-            if minimum(lr2) - maximum(lr1) > k_angular_max
-                continue
-            end
-
-            nus2 = states_nu[id2]
-            # Skip if all contributions of the two states are far apart in n and None of them is low-n
-            if all(abs(nu1-nu2) >= 11 for nu1 in nus1 for nu2 in nus2) &&
-               all(nu1 > 25 for nu1 in nus1) &&
-               all(nu2 > 25 for nu2 in nus2)
-                continue
-            end
-
-            m = MQDT.multipole_moments(s1, s2, parameters)
-            # multipole_moments returns the matrix elements in the following order
-            # electric dipole, electric quadrupole, diamagnetic, magnetic
-            table_keys = [
-                "matrix_elements_d",
-                "matrix_elements_q",
-                "matrix_elements_q0",
-                "matrix_elements_mu",
-            ]
-            prefactor_transposed = (-1)^(s2.f - s1.f)
-
-            for (i, key) in enumerate(table_keys)
-                if m[i] != 0
-                    # start IDs from 0 for consistency with python
-                    _id1 = id1 - 1 + START_ID
-                    _id2 = id2 - 1 + START_ID
-                    push!(row_col_value[key], (_id1, _id2, m[i]))
-                    if id1 != id2
-                        push!(row_col_value[key], (_id2, _id1, m[i] * prefactor_transposed))
-                    end
-                end
-            end
-
-        end
-    end
-
-    return row_col_value
-end
-
-
-function rcv_to_df(row_col_value::Vector{Tuple{Int64,Int64,Float64}})
-    """Convert a row_col_value to a DataFrame."""
-    id_initial = [m[1] for m in row_col_value]
-    id_final = [m[2] for m in row_col_value]
-    val = [m[3] for m in row_col_value]
-    df = DataFrame(id_initial = id_initial, id_final = id_final, val = val)
-    return df
-end
-
-
-function basis_to_df(T::MQDT.BasisArray, P::MQDT.Parameters)
-    df = DataFrame(
-        id = collect(START_ID:(size(T)-1+START_ID)),
-        energy = MQDT.get_e(T, P) / 219474.6313632,  # convert 1/cm to atomic units
-        parity = MQDT.get_p(T),
-        n = get_n(T, P),
-        nu = MQDT.get_nu(T),
-        f = MQDT.get_f(T),
-        exp_nui = exp_nui(T),
-        exp_l = calc_exp_qn(T, "l_tot"),
-        exp_j = calc_exp_qn(T, "j_tot"),
-        exp_s = calc_exp_qn(T, "s_tot"),
-        exp_l_ryd = calc_exp_qn(T, "l_r"),
-        exp_j_ryd = calc_exp_qn(T, "j_r"),
-        std_nui = std_nui(T),
-        std_l = calc_std_qn(T, "l_tot"),
-        std_j = calc_std_qn(T, "j_tot"),
-        std_s = calc_std_qn(T, "s_tot"),
-        std_l_ryd = calc_std_qn(T, "l_r"),
-        std_j_ryd = calc_std_qn(T, "j_r"),
-        is_j_total_momentum = repeat([iszero(P.spin)], size(T)),
-        is_calculated_with_mqdt = is_mqdt(T),
-        underspecified_channel_contribution = get_neg(T),
-    )
-    return df
-end
-
-
-function exp_nui(T::MQDT.BasisArray)
-    t = Vector{Float64}(undef, size(T))
-    for (i, state) in enumerate(T.states)
-        t[i] = exp_q(state.nu_list, state.coefficients)
-    end
-    return t
-end
-
-function std_nui(T::MQDT.BasisArray)
-    t = Vector{Float64}(undef, size(T))
-    for (i, state) in enumerate(T.states)
-        t[i] = std_q(state.nu_list, state.coefficients)
-    end
-    return t
-end
-
-function is_mqdt(T::MQDT.BasisArray)
-    t = Vector{Bool}(undef, size(T))
-    for (i, state) in enumerate(T.states)
-        t[i] = !isone(length(state.coefficients))
-    end
-    return t
-end
-
-
-function get_neg(T::MQDT.BasisArray)
-    t = Vector{Float64}(undef, size(T))
-    for (i, state) in enumerate(T.states)
-        irrel = findall(iszero, state.model.core)
-        t[i] = sum(state.coefficients[irrel] .^ 2)
-    end
-    return t
-end
-
-function exp_q(q::Vector, n::Vector)
-    if allequal(q)
-        return Float64(q[1])
-    else
-        m = n .^ 2
-        M = sum(m)
-        if M > 1
-            m /= M
-        end
-        return LinearAlgebra.dot(q, m)
-    end
-end
-
-function std_q(q::Vector, n::Vector)
-    if allequal(q)
-        return 0.0
-    else
-        m = n .^ 2
-        M = sum(m)
-        if M > 1
-            m /= M
-        end
-        e1 = LinearAlgebra.dot(q, m)^2
-        e2 = LinearAlgebra.dot(q .^ 2, m)
-        if abs(e1 - e2) < 1e-11
-            return 0.0
-        else
-            return sqrt(e2 - e1)
-        end
-    end
-end
-
-function get_n(T::MQDT.BasisArray, P::MQDT.Parameters)
-    nu = MQDT.get_nu(T)
-    l = round.(Int, calc_exp_qn(T, "l_r"))
-    return get_n(nu, l, P.species)
-end
-
-function get_n(nu::Vector{Float64}, l::Vector{Int}, species::Symbol)
-    i0 = findall(iszero, l)
-    i1 = findall(iszero, l .- 1)
-    i2 = findall(iszero, l .- 2)
-    i3 = findall(iszero, l .- 3)
-    j0 = findall(x->x<2, nu)
-    nu[j0] .+= 1
-    if occursin("Yb", String(species))
-        nu[i0] .+= 4
-        nu[i1] .+= 3
-        nu[i2] .+= 2
-        nu[i3] .+= 1
-    else
-        nu[i0] .+= 3
-        nu[i1] .+= 2
-        nu[i2] .+= 2
-    end
-    return ceil.(Int, nu)
-end
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..faaf01c
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1466 @@
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