PR Review: remove add_dimension_coordinate

.devcontainer/Dockerfile.cli

@@ -0,0 +1,47 @@
+# HOW TO BUILD AND RUN THIS DOCKERFILE
+# * Clone mdio-python and build a Docker image:
+#      git clone https://github.com/TGSAI/mdio-python.git
+#      cd mdio-python
+#      docker build -t mdio-cli -f .devcontainer/Dockerfile.cli . 
+# * Run /bin/bash in the Docker container:
+#
+#
+# USAGE:
+#  docker run -it --rm --name mdio-cli mdio-cli --version
+#  docker run -it --rm --name mdio-cli mdio-cli --help
+#
+#  LOCAL_DATA_DIR=$(pwd); \
+#  docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --name mdio-cli mdio-cli \
+#     segy import \
+#     /DATA/segy_file.segy \
+#     /DATA/mdio_file.mdio \
+#     -loc 181,185 \
+#     -names inline,crossline
+#
+#  LOCAL_DATA_DIR=$(pwd); \
+#  docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --name mdio-cli mdio-cli \
+#     segy export \
+#     /DATA/mdio_file.mdio \
+#     /DATA/segy_file_copy.segy
+#
+FROM python:3.13-bookworm
+# Create the user (https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user)
+ENV USERNAME=python
+ENV USER_UID=1000
+ENV USER_GID=$USER_UID
+RUN groupadd --gid $USER_GID $USERNAME && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME 
+
+# Set the default non-root user
+USER $USERNAME
+
+# Add path to the user-installed packages
+ENV PYTHONUSERBASE=/home/$USERNAME/.local
+ENV PATH="$PYTHONUSERBASE/bin:$PATH"
+
+COPY --chown=$USERNAME:$USERNAME ./ /home/$USERNAME/mdio-python
+
+WORKDIR /home/$USERNAME/mdio-python
+RUN pip install .
+
+ENTRYPOINT ["mdio"]
+CMD ["--version"]

.devcontainer/Dockerfile.dev

@@ -0,0 +1,61 @@
+# USAGE: 
+#   This file will be used by the VS Code DevContainer extension 
+#   to create a development environment for the mdio-python project.
+# HOW TO RUN TESTS
+#    1. Open the project in VS Code.
+#    2. Open the Command Palette (Ctrl+Shift+P) and select "Dev Containers: Reopen in Container".
+#    3. Once the container is running, open a terminal in VS Code.
+#    4. Run the tests using the command: `nox -s test`.
+# HOW TO MANUALLY BUILD AND RUN THE CONTAINER
+#    docker build -t mdio-dev -f .devcontainer/Dockerfile.dev .
+#    docker run -it --rm --entrypoint /bin/bash --name mdio-dev mdio-dev
+# NOTES: 
+#  1. The container will be run as the non-root user 'vscode' with UID 1000.
+#  2. The virtual environment will be setup at /home/vscode/venv 
+#  3. The project source code will be mounted at /workspaces/mdio-python
+ARG PYTHON_VERSION="3.13"
+ARG LINUX_DISTRO="bookworm"
+ARG UV_VERSION="0.6.11"
+ARG NOX_VERSION="2025.2.9"
+FROM mcr.microsoft.com/devcontainers/python:1-${PYTHON_VERSION}-${LINUX_DISTRO}
+
+# Install git for nox pre-commit
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    git \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV USERNAME="vscode"
+USER $USERNAME
+
+# # Add path to the user-installed packages
+# ENV PYTHONUSERBASE=/home/$USERNAME/.local
+# ENV PATH="$PYTHONUSERBASE/bin:$PATH"
+
+COPY --chown=$USERNAME:$USERNAME ./ /workspaces/mdio-python
+
+WORKDIR /workspaces/mdio-python
+
+ARG UV_VERSION
+ARG NOX_VERSION
+RUN python3 -m pip install uv==${UV_VERSION} nox==${NOX_VERSION} msgpack ipykernel
+
+# Initialize virtual environement in the container
+ENV VIRTUAL_ENV="/home/$USERNAME/venv"
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# installing pytest is required for VS Code Python Testing
+RUN pip install pytest pytest-cov pytest-mock pytest-asyncio
+
+# Install the project in editable mode
+# This allows for live reloading of the code during development
+RUN pip install -e .
+
+# RUN uv pip install snakeviz
+
+
+
+
+
+

.devcontainer/Dockerfile.nox

@@ -0,0 +1,49 @@
+# HOW TO BUILD AND RUN THIS DOCKERFILE
+# 1. Make sure you have Docker installed and running.
+# 2. Clone mdio-python and build the Docker image:
+#    git clone https://github.com/TGSAI/mdio-python.git
+#    cd mdio-python
+#    docker build -t mdio-nox -f .devcontainer/Dockerfile.nox .
+# 3. Run /bin/bash in the Docker container :
+#    LOCAL_DATA_DIR=$(pwd); \
+#    docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --entrypoint /bin/bash --name mdio-nox mdio-nox
+#
+# USAGE:
+#   docker run -it --rm mdio-nox --list
+#   docker run -it --rm mdio-nox -s tests-3.13
+#   docker run -it --rm mdio-nox --no-stop-on-first-error
+#
+# NOTE: nox will fail if run in the directory mounted from the host machine
+ARG PYTHON_VERSION="3.13"
+ARG LINUX_DISTRO="bookworm"
+ARG UV_VERSION="0.6.11"
+ARG NOX_VERSION="2025.2.9"
+FROM python:${PYTHON_VERSION}-${LINUX_DISTRO}
+ARG PYTHON_VERSION
+ARG LINUX_DISTRO
+RUN echo "Using python:${PYTHON_VERSION}-${LINUX_DISTRO}"
+# Create the user (https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user)
+ENV USERNAME=python
+ENV USER_UID=1000
+ENV USER_GID=$USER_UID
+RUN groupadd --gid $USER_GID $USERNAME && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME
+# Set the default non-root user
+USER $USERNAME
+
+# Add path to the user-installed packages
+ENV PYTHONUSERBASE=/home/$USERNAME/.local
+ENV PATH="$PYTHONUSERBASE/bin:$PATH"
+
+COPY --chown=$USERNAME:$USERNAME ./ /home/$USERNAME/mdio-python
+
+WORKDIR /home/$USERNAME/mdio-python
+RUN pip install .
+
+# Install UV dependency manager and Nox test automator
+ARG UV_VERSION
+ARG NOX_VERSION
+RUN echo "Using uv: $UV_VERSION and nox: $NOX_VERSION"
+RUN python3 -m pip install uv==${UV_VERSION} nox==${NOX_VERSION} msgpack ipykernel
+
+ENTRYPOINT ["nox"]
+CMD ["--list"]

.devcontainer/devcontainer.json

@@ -2,12 +2,12 @@
 // README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
   "build": {
-    "dockerfile": "Dockerfile",
+    "dockerfile": "Dockerfile.dev",
     "context": ".."
   },
   // Use 'postCreateCommand' to run commands after the container is created.
   "postCreateCommand": {
-    "post_create_script": "bash ./.devcontainer/post-install.sh"
+    // "post_create_script": "bash ./.devcontainer/post-install.sh"
   },
   // Forward 8787 to enable us to view dask dashboard
   "forwardPorts": [8787],
@@ -16,8 +16,9 @@
     // Configure properties specific to VS Code.
     "vscode": {
       "settings": {
-        "python.terminal.activateEnvInCurrentTerminal": true,
-        "python.defaultInterpreterPath": "/opt/venv/bin/python"
+      "python.testing.pytestArgs": ["tests"], 
+          "python.testing.unittestEnabled": false,
+          "python.testing.pytestEnabled": true
       },
       "extensions": [
         "ms-python.python",
@@ -27,17 +28,18 @@
         "ms-toolsai.jupyter-renderers",
         "vscode-icons-team.vscode-icons",
         "wayou.vscode-todo-highlight",
-        "streetsidesoftware.code-spell-checker"
+        "streetsidesoftware.code-spell-checker",
+        "eamodio.gitlens",
+        "visualstudioexptteam.vscodeintellicode"
       ]
     }
   },
   // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
   // "remoteUser": "root",
   "updateRemoteUserUID": true,
+  "workspaceMount": "source=${localWorkspaceFolder},target=/workspaces/mdio-python,type=bind",
+  "workspaceFolder": "/workspaces/mdio-python",
   "mounts": [
-    // Re-use local Git configuration
-    "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig_tmp,type=bind,consistency=cached",
-    "source=${localEnv:HOME}/.gitconfig,target=/root/.gitconfig_tmp,type=bind,consistency=cached",
-    "source=${localEnv:SCRATCH_DIR}/${localEnv:USER},target=/scratch/,type=bind,consistency=cached"
+    // "source=${localWorkspaceFolder}/../DATA/,target=/DATA/,type=bind,consistency=cached"
   ]
 }

src/mdio/schemas/v1/dataset_builder.py

@@ -245,30 +245,6 @@ def add_coordinate(  # noqa: PLR0913
         self._state = _BuilderState.HAS_COORDINATES
         return self
 
-    def add_dimension_coordinate(
-        self,
-        dimension_name: str,
-        *,
-        data_type: ScalarType,
-        compressor: Blosc | ZFP | None = None,
-        metadata_info: VariableMetadataList | None = None,
-    ) -> "MDIODatasetBuilder":
-        """Add a dimension coordinate variable for a pre-existing dimension.
-        This is a convenience method to create a coordinate variable
-        that represents sampling along a dimension.
-
-        The dimension coordinate is a coordinate that has a single dimension and
-        the name of the coordinate is the same as the name of the dimension
-        """
-        self.add_coordinate(dimension_name,
-                            long_name=dimension_name,
-                            dimensions=[dimension_name],
-                            data_type=data_type,
-                            compressor=compressor,
-                            metadata_info=_to_dictionary(metadata_info))
-
-        return self
-
     def add_variable(  # noqa: PLR0913
         self,
         name: str,

tests/unit/v1/test_dataset_builder_add_variable.py

@@ -97,8 +97,8 @@ def test_add_variable_with_coords() -> None:
     builder.add_dimension("depth", 300)
 
     # Add dimension coordinates before we can add a data variable
-    builder.add_dimension_coordinate("inline", data_type=ScalarType.INT32)
-    builder.add_dimension_coordinate("crossline", data_type=ScalarType.INT32)
+    builder.add_coordinate("inline", dimensions=["inline"], data_type=ScalarType.UINT32)
+    builder.add_coordinate("crossline", dimensions=["crossline"], data_type=ScalarType.UINT32)
 
     # Validate: adding a variable with a coordinate that has not been pre-created is not allowed
     msg = "Pre-existing coordinate named 'depth' is not found"
@@ -168,32 +168,6 @@ def test_add_variable_with_coords() -> None:
     assert builder._get_coordinate(var_ampl2.coordinates, "cdp-y") is not None
 
 
-def test_add_dimension_coordinate() -> None:
-    """Test adding dimension variable."""
-    builder = MDIODatasetBuilder("test_dataset")
-    builder.add_dimension("inline", 100)
-
-    builder.add_dimension_coordinate("inline", data_type=ScalarType.INT32)
-
-    # Validate: that coordinate is stored in the builder global list
-    coord_il = builder._get_coordinate(builder._coordinates, "inline")
-    # Validate: that dimensions are stored as NamedDimensions in the coordinate
-    assert _get_named_dimension(coord_il.dimensions, "inline", 100) is not None
-    # Validate: a dim variable has been created
-    var_il = next((e for e in builder._variables if e.name == "inline"), None)
-    assert var_il is not None
-    # Validate: the variable has the expected properties
-    assert var_il.name == "inline"
-    assert var_il.long_name == "'inline' coordinate variable"
-    assert len(var_il.dimensions) == 1
-    assert _get_named_dimension(var_il.dimensions, "inline", 100) is not None
-    assert var_il.data_type == ScalarType.INT32
-    assert var_il.compressor is None  # Default value
-    assert len(var_il.coordinates) == 1
-    assert builder._get_coordinate(var_il.coordinates, "inline") is not None
-    assert var_il.metadata is None  # Default value
-
-
 def test_add_variable_with_defaults() -> None:
     """Test adding variable with default arguments."""
     builder = MDIODatasetBuilder("test_dataset")
@@ -202,12 +176,12 @@ def test_add_variable_with_defaults() -> None:
     builder.add_dimension("crossline", 200)
     builder.add_dimension("depth", 300)
     # Add dimension coordinates
-    builder.add_dimension_coordinate("inline", data_type=ScalarType.INT32)
-    builder.add_dimension_coordinate("crossline", data_type=ScalarType.INT32)
-    builder.add_dimension_coordinate("depth",
-                                     data_type=ScalarType.FLOAT32,
-                                     metadata_info=[
-                                         AllUnits(units_v1=LengthUnitModel(length=LengthUnitEnum.METER))])
+    builder.add_coordinate("inline", dimensions=["inline"], data_type=ScalarType.UINT32)
+    builder.add_coordinate("crossline", dimensions=["crossline"], data_type=ScalarType.UINT32)
+    builder.add_coordinate("depth", dimensions=["depth"], data_type=ScalarType.UINT32,
+                           metadata_info=[
+                               AllUnits(units_v1=LengthUnitModel(length=LengthUnitEnum.METER))
+                           ]) 
 
     # Add data variable using defaults
     builder.add_variable("ampl",
@@ -244,10 +218,10 @@ def test_add_variable_full_parameters() -> None:
     builder.add_dimension("depth", 300)
 
     # Add dimension coordinates
-    builder.add_dimension_coordinate("inline", data_type=ScalarType.INT32)
-    builder.add_dimension_coordinate("crossline", data_type=ScalarType.INT32)
-    builder.add_dimension_coordinate("depth", data_type=ScalarType.INT32)
-    
+    builder.add_coordinate("inline", dimensions=["inline"], data_type=ScalarType.UINT32)
+    builder.add_coordinate("crossline", dimensions=["crossline"], data_type=ScalarType.UINT32)
+    builder.add_coordinate("depth", dimensions=["depth"], data_type=ScalarType.UINT32)
+
     # Add coordinates before we can add a data variable
     builder.add_coordinate("cdp-x", dimensions=["inline", "crossline"], data_type=ScalarType.FLOAT64)
     builder.add_coordinate("cdp-y", dimensions=["inline", "crossline"], data_type=ScalarType.FLOAT64)

tests/unit/v1/test_dataset_builder_build.py

@@ -31,10 +31,8 @@ def test_build() -> None:
         MDIODatasetBuilder("test_dataset")
         .add_dimension("inline", 100)
         .add_dimension("crossline", 200)
-        # Add a dimension coordinate explicitly using add_coordinate()
         .add_coordinate("inline", dimensions=["inline"], data_type=ScalarType.FLOAT64) 
-        # Add a dimension coordinate using .add_dimension_coordinate() shortcut
-        .add_dimension_coordinate("crossline", data_type=ScalarType.FLOAT64)
+        .add_coordinate("crossline", dimensions=["crossline"], data_type=ScalarType.FLOAT64) 
         .add_coordinate("x_coord", dimensions=["inline", "crossline"])
         .add_coordinate("y_coord", dimensions=["inline", "crossline"])
         .add_variable("data", 
@@ -176,12 +174,12 @@ def make_campos_3d_dataset() -> Dataset:
     ds.add_dimension("inline", 256)
     ds.add_dimension("crossline", 512)
     ds.add_dimension("depth", 384)
-    ds.add_dimension_coordinate("inline", data_type=ScalarType.UINT32)
-    ds.add_dimension_coordinate("crossline", data_type=ScalarType.UINT32)
-    ds.add_dimension_coordinate("depth", data_type=ScalarType.FLOAT64,
-                                metadata_info=[
-                                    AllUnits(units_v1=LengthUnitModel(length=LengthUnitEnum.METER))
-                                    ])
+    ds.add_coordinate("inline", dimensions=["inline"], data_type=ScalarType.UINT32) 
+    ds.add_coordinate("crossline", dimensions=["crossline"], data_type=ScalarType.UINT32) 
+    ds.add_coordinate("depth", dimensions=["depth"], data_type=ScalarType.FLOAT64, 
+                      metadata_info=[
+                          AllUnits(units_v1=LengthUnitModel(length=LengthUnitEnum.METER))
+                      ])
     # Add coordinates
     ds.add_coordinate(
         "cdp-x",