Zarr v3 Engine (#530)

* correct typo in cli doc

* fix type hint for None storage opts

* zarr v3 dependency

* zarr v3 support

* Update type annotations for create_zarr_hierarchy method

* remove memory cache usage

* update api usage

* use cloud segy in quickstart

* Fix writer usage and make rechunk work with v3

* update notebooks

* fix bug in copy

* remove duplicate zarr dependency

Co-authored-by: Brian Michell <[email protected]>

* remove notebook

* add convenience test file to vcs

* Remove unused API version retrieval logic.

* Refactor function signatures by removing unused parameters.

* Refine docstring in SEG-Y to MDIO conversion function

* Refactor header dtype initialization in factory.py

* test only full copy in integration

* Add warning filter to suppress chunk size balancing warnings

* use more readable expression

Co-authored-by: Brian Michell <[email protected]>

---------

Co-authored-by: Brian Michell <[email protected]>

Author: tasansal

.github/workflows/tests.yml

@@ -17,17 +17,14 @@ jobs:
           #          - { python: "3.13", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.12", os: "ubuntu-latest", session: "mypy" }
           #          - { python: "3.11", os: "ubuntu-latest", session: "mypy" }
-          #          - { python: "3.10", os: "ubuntu-latest", session: "mypy" }
           - { python: "3.13", os: "ubuntu-latest", session: "tests" }
           - { python: "3.12", os: "ubuntu-latest", session: "tests" }
           - { python: "3.11", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.10", os: "ubuntu-latest", session: "tests" }
           - { python: "3.13", os: "windows-latest", session: "tests" }
           - { python: "3.13", os: "macos-latest", session: "tests" }
           #          - { python: "3.13", os: "ubuntu-latest", session: "typeguard" }
           #          - { python: "3.12", os: "ubuntu-latest", session: "typeguard" }
           #          - { python: "3.11", os: "ubuntu-latest", session: "typeguard" }
-          #          - { python: "3.10", os: "ubuntu-latest", session: "typeguard" }
           #          - { python: "3.13", os: "ubuntu-latest", session: "xdoctest" }
           - { python: "3.13", os: "ubuntu-latest", session: "docs-build" }
 

docs/notebooks/creation.ipynb

@@ -27,8 +27,8 @@
      "name": "#%%\n"
     },
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:13.251380Z",
-     "start_time": "2025-04-10T23:01:13.249206Z"
+     "end_time": "2025-04-16T14:50:04.371422Z",
+     "start_time": "2025-04-16T14:50:04.368107Z"
     }
    },
    "source": [
@@ -75,8 +75,8 @@
      "name": "#%%\n"
     },
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:15.001483Z",
-     "start_time": "2025-04-10T23:01:14.852174Z"
+     "end_time": "2025-04-16T14:50:06.121450Z",
+     "start_time": "2025-04-16T14:50:06.002634Z"
     }
    },
    "source": [
@@ -94,7 +94,7 @@
     "    name=\"chunked_012\",\n",
     "    dtype=\"float32\",\n",
     "    chunks=(128, 128, 128),\n",
-    "    compressor=compressor,\n",
+    "    compressors=compressor,\n",
     "    header_dtype=header_dtype,\n",
     ")\n",
     "\n",
@@ -127,8 +127,8 @@
      "name": "#%%\n"
     },
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:20.800890Z",
-     "start_time": "2025-04-10T23:01:20.755989Z"
+     "end_time": "2025-04-16T14:50:09.974442Z",
+     "start_time": "2025-04-16T14:50:09.951257Z"
     }
    },
    "source": [
@@ -147,7 +147,7 @@
        "  'C03                                                                             ',\n",
        "  'C04                                                                             '],\n",
        " {},\n",
-       " {'rms': 0, 'max': 0, 'mean': 0, 'std': 0, 'min': 0})"
+       " {'rms': 0, 'min': 0, 'mean': 0, 'max': 0, 'std': 0})"
       ]
      },
      "execution_count": 4,
@@ -181,13 +181,13 @@
      "name": "#%%\n"
     },
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:22.957564Z",
-     "start_time": "2025-04-10T23:01:22.431939Z"
+     "end_time": "2025-04-16T14:50:12.498287Z",
+     "start_time": "2025-04-16T14:50:11.670230Z"
     }
    },
    "source": [
     "sample_dim = writer.grid.select_dim(\"sample\")\n",
-    "sample_interval = sample_dim.coords[1] - sample_dim.coords[0]\n",
+    "sample_interval = int(sample_dim.coords[1] - sample_dim.coords[0])\n",
     "num_samples = sample_dim.size\n",
     "writer.binary_header = {\n",
     "    \"data_sample_format\": 1,\n",
@@ -218,7 +218,7 @@
        "  'samples_per_trace': 750,\n",
        "  'segy_revision_major': 1,\n",
        "  'segy_revision_minor': 0},\n",
-       " {'rms': 3, 'max': 4, 'mean': 12, 'std': 5, 'min': -4})"
+       " {'rms': 3, 'min': -4, 'mean': 12, 'max': 4, 'std': 5})"
       ]
      },
      "execution_count": 5,
@@ -237,8 +237,8 @@
    "cell_type": "code",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:24.496155Z",
-     "start_time": "2025-04-10T23:01:24.214141Z"
+     "end_time": "2025-04-16T14:50:14.256953Z",
+     "start_time": "2025-04-16T14:50:14.036094Z"
     }
    },
    "source": [
@@ -279,8 +279,8 @@
    "cell_type": "code",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:28.673420Z",
-     "start_time": "2025-04-10T23:01:26.174688Z"
+     "end_time": "2025-04-16T14:50:15.788812Z",
+     "start_time": "2025-04-16T14:50:15.009889Z"
     }
    },
    "source": [
@@ -298,8 +298,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Unwrapping MDIO Blocks: 100%|██████████| 7/7 [00:02<00:00,  2.99it/s]\n",
-      "Merging lines: 100%|██████████| 1/1 [00:00<00:00, 24.22it/s]"
+      "Unwrapping MDIO Blocks: 100%|██████████| 7/7 [00:00<00:00, 10.55it/s]\n",
+      "Merging lines: 100%|██████████| 1/1 [00:00<00:00, 17.26it/s]"
      ]
     },
     {
@@ -351,8 +351,8 @@
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-04-10T23:01:30.367161Z",
-     "start_time": "2025-04-10T23:01:30.229117Z"
+     "end_time": "2025-04-16T14:50:17.246513Z",
+     "start_time": "2025-04-16T14:50:17.111779Z"
     }
    },
    "cell_type": "code",
@@ -369,6 +369,13 @@
    ],
    "outputs": [],
    "execution_count": 8
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": ""
   }
  ],
  "metadata": {