Move config inside of package such that it is accessible as a default

.github/workflows/gitlab.yml

@@ -6,13 +6,11 @@ on:
       paths:
         - "exact_kmeans/**"
         - "tests/**"
-        - "config/**"
         - "poetry.lock"
     pull_request:
       paths:
         - "exact_kmeans/**"
         - "tests/**"
-        - "config/**"
         - "poetry.lock"
     # Allows you to run this workflow manually from the Actions tab
     workflow_dispatch:

.github/workflows/mypy-flake-test.yml

@@ -7,13 +7,11 @@ on:
     paths:
       - "exact_kmeans/**"
       - "tests/**"
-      - "config/**"
       - "poetry.lock"
   pull_request:
     paths:
       - "exact_kmeans/**"
       - "tests/**"
-      - "config/**"
       - "poetry.lock"
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:

README.md

@@ -25,7 +25,7 @@ ILP#2 gets cluster sizes $c_1,\ldots, c_i$ with $2\leq i\leq k$ as input. If $c_
 
 To search for the cluster sizes of an optimal solution we use a branch and bound approach. In a branch node of level $i$ the $i$ largest cluster sizes $c_1, \ldots, c_i$ are already fixed. The variables `branching_levels` and `fill_cluster_sizes` define the behavior on these branching nodes. If `branching_levels` is greater equal to the level $i$ of the node then we use ILP#2 to bound the current cost and decide if we branch, otherwise we always branch on this node. If the variable `fill_cluster_sizes` is set to true we compute the smallest possible remaining cluster sizes $c_{i+1},\ldots, c_{k}$ and run ILP#2 with cluster sizes $c_1,\ldots, c_k$. If the variable `fill_cluster_sizes` is set to false we run ILP#2 only with the fixed cluster sizes $c_1,\ldots, c_i$. Setting `fill_cluster_sizes` to true may lead to less branching but can increase the solving time of ILP#2.
 
-To customize the runs, you can create a config file. The default config file is [`config/default.yaml`](config/default.yaml). You can also pass a different config file as an argument.
+To customize the runs, you can create a config file. The default config file is [`exact_kmeans/config/default.yaml`](exact_kmeans/config/default.yaml). You can also pass a different config file as an argument.
 - `num_processes` (integer or float) sets the number of processes used. The algorithm was parallelized using the `multiprocessing` package, so you can set the number of processes that you want to use. If you use an integer, at most that number of processes will be taken, otherwise if you use a float, it will be a fraction of the available CPUs. If the parameter is not passed, the algorithm will use all available CPUs.
 - `bound_model_params` are the arguments that are passed to the ILP#1 model. Please have a look at the [Gurobi documentation](https://www.gurobi.com/documentation/9.1/refman/parameters.html) for more information.
 - `model_params` are the arguments that are passed to the ILP#2 model. Please have a look at the [Gurobi documentation](https://www.gurobi.com/documentation/9.1/refman/parameters.html) for more information.
@@ -90,7 +90,7 @@ poetry install
 
 Run the program
 ```bash
-poetry run python -m exact_kmeans --data-path iris.csv --verbose --results-path test/iris.json --k 3 --config-file config/default.yaml
+poetry run python -m exact_kmeans --data-path iris.csv --verbose --results-path test/iris.json --k 3 --config-file exact_kmeans/config/default.yaml
 ```
 
 Your `data-path` should be a file with a header containing only the comma-separated data points. Example:

exact_kmeans/__main__.py

@@ -39,7 +39,9 @@ def set_up_logger(log_file: Path, mode: str = "w+") -> None:
 
     parser.add_argument("--k", type=int, required=True)
     parser.add_argument("--data-path", type=Path, required=True)
-    parser.add_argument("--config-file", type=Path, default="config/default.yaml")
+    parser.add_argument(
+        "--config-file", type=Path, default="exact_kmeans/config/default.yaml"
+    )
     parser.add_argument("--kmeans-iterations", type=int, default=100)
     parser.add_argument("--results-path", type=Path, default=None)
     parser.add_argument("--load-existing-run-path", type=Path, default=None)

exact_kmeans/ilp.py

@@ -51,9 +51,7 @@ def __init__(
         self,
         X: Union[np.ndarray, pd.DataFrame],
         k: int,
-        config_file: Union[str, Path] = Path(
-            os.path.split(__file__)[0]
-        ).parent.resolve()
+        config_file: Union[str, Path] = Path(__file__).parent.resolve()
         / "config"
         / "default.yaml",
         cache_current_run_path: Optional[Path] = None,
@@ -69,8 +67,6 @@ def __init__(
         self.k = k
         self.n = len(X)
 
-        # self.dmax = compute_largest_distance(X)
-
         self._v = 1
         self._n = self.n + self._v
         self._k = self.k + self._v