remove contact sites; update dracopy interface

Dockerfile

@@ -1,8 +1,6 @@
-# FROM gcr.io/neuromancer-seung-import/pychunkedgraph:graph-tool_dracopy
-FROM seunglab/pychunkedgraph:graph-tool_dracopy
+FROM caveconnectome/pychunkedgraph:base_042124
 COPY override/timeout.conf /etc/nginx/conf.d/timeout.conf
 COPY override/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
 COPY requirements.txt /app
-RUN pip install --upgrade pip \
-    && pip install --no-cache-dir --upgrade -r requirements.txt
+RUN pip install --no-cache-dir -r requirements.txt
 COPY . /app

cloudbuild.yaml

@@ -1,31 +1,25 @@
 steps:
+  # Login to Docker Hub
   - name: "gcr.io/cloud-builders/docker"
     entrypoint: "bash"
     args: ["-c", "docker login --username=$$USERNAME --password=$$PASSWORD"]
     secretEnv: ["USERNAME", "PASSWORD"]
-  # - name: 'gcr.io/cloud-builders/docker'
-  #   args: [ 'build', '-t', 'gcr.io/$PROJECT_ID/pychunkedgraph', '.' ]
+
   - name: "gcr.io/cloud-builders/docker"
     entrypoint: "bash"
     args:
       - "-c"
       - |
-        docker build -t gcr.io/$PROJECT_ID/pychunkedgraph:$TAG_NAME .
+        docker build -t $$USERNAME/pychunkedgraph:$TAG_NAME .
     timeout: 600s
-  - name: "gcr.io/cloud-builders/docker"
-    entrypoint: "bash"
-    args:
-      [
-        "-c",
-        "docker tag gcr.io/$PROJECT_ID/pychunkedgraph:$TAG_NAME $$USERNAME/pychunkedgraph:$TAG_NAME",
-      ]
     secretEnv: ["USERNAME"]
+
+  # Push the final image to Dockerhub
   - name: "gcr.io/cloud-builders/docker"
     entrypoint: "bash"
     args: ["-c", "docker push $$USERNAME/pychunkedgraph:$TAG_NAME"]
     secretEnv: ["USERNAME"]
-images:
-  - "gcr.io/$PROJECT_ID/pychunkedgraph:$TAG_NAME"
+
 availableSecrets:
   secretManager:
     - versionName: projects/$PROJECT_ID/secrets/docker-password/versions/1

pychunkedgraph/app/app_utils.py

@@ -250,7 +250,7 @@ def ccs(coordinates_nm_):
         ccs = [np.array(list(cc)) for cc in nx.connected_components(graph)]
         return ccs
 
-    coordinates = np.array(coordinates, dtype=np.int)
+    coordinates = np.array(coordinates, dtype=int)
     coordinates_nm = coordinates * cg.cv.resolution
 
     node_ids = np.array(node_ids, dtype=np.uint64)

pychunkedgraph/app/meshing/common.py

@@ -72,7 +72,7 @@ def handle_get_manifest(table_id, node_id):
     if "bounds" in request.args:
         bounds = request.args["bounds"]
         bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
+            [b.split("-") for b in bounds.split("_")], dtype=int
         ).T
     else:
         bounding_box = None

pychunkedgraph/app/segmentation/common.py

@@ -18,7 +18,7 @@
 from pychunkedgraph.backend import history as cg_history
 from pychunkedgraph.backend import lineage
 from pychunkedgraph.backend.utils import column_keys, basetypes
-from pychunkedgraph.graph_analysis import analysis, contact_sites
+from pychunkedgraph.graph_analysis import analysis
 from pychunkedgraph.backend.graphoperation import GraphEditOperation
 
 __api_versions__ = [0, 1]
@@ -516,7 +516,7 @@ def handle_leaves(table_id, root_id):
     if "bounds" in request.args:
         bounds = request.args["bounds"]
         bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
+            [b.split("-") for b in bounds.split("_")], dtype=int
         ).T
     else:
         bounding_box = None
@@ -559,7 +559,7 @@ def handle_leaves_many(table_id):
     if "bounds" in request.args:
         bounds = request.args["bounds"]
         bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
+            [b.split("-") for b in bounds.split("_")], dtype=int
         ).T
     else:
         bounding_box = None
@@ -591,7 +591,7 @@ def handle_leaves_from_leave(table_id, atomic_id):
     if "bounds" in request.args:
         bounds = request.args["bounds"]
         bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
+            [b.split("-") for b in bounds.split("_")], dtype=int
         ).T
     else:
         bounding_box = None
@@ -618,7 +618,7 @@ def handle_subgraph(table_id, root_id):
     if "bounds" in request.args:
         bounds = request.args["bounds"]
         bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
+            [b.split("-") for b in bounds.split("_")], dtype=int
         ).T
     else:
         bounding_box = None
@@ -847,66 +847,6 @@ def oldest_timestamp(table_id):
     return earliest_timestamp
 
 
-### CONTACT SITES --------------------------------------------------------------
-
-
-def handle_contact_sites(table_id, root_id):
-    partners = request.args.get("partners", True, type=app_utils.toboolean)
-    as_list = request.args.get("as_list", True, type=app_utils.toboolean)
-    areas_only = request.args.get("areas_only", True, type=app_utils.toboolean)
-
-    current_app.table_id = table_id
-    user_id = str(g.auth_user["id"])
-    current_app.user_id = user_id
-
-    timestamp = _parse_timestamp(
-        "timestamp", default_timestamp=time.time(), return_datetime=True
-    )
-
-    if "bounds" in request.args:
-        bounds = request.args["bounds"]
-        bounding_box = np.array(
-            [b.split("-") for b in bounds.split("_")], dtype=np.int
-        ).T
-    else:
-        bounding_box = None
-
-    # Call ChunkedGraph
-    cg = app_utils.get_cg(table_id)
-
-    cs_list, cs_metadata = contact_sites.get_contact_sites(
-        cg,
-        np.uint64(root_id),
-        bounding_box=bounding_box,
-        compute_partner=partners,
-        end_time=timestamp,
-        as_list=as_list,
-        areas_only=areas_only,
-    )
-
-    return cs_list, cs_metadata
-
-
-def handle_pairwise_contact_sites(table_id, first_node_id, second_node_id):
-    current_app.request_type = "pairwise_contact_sites"
-    current_app.table_id = table_id
-    user_id = str(g.auth_user["id"])
-    current_app.user_id = user_id
-
-    timestamp = _parse_timestamp("timestamp", time.time(), return_datetime=True)
-
-    exact_location = request.args.get("exact_location", True, type=app_utils.toboolean)
-    cg = app_utils.get_cg(table_id)
-    contact_sites_list, cs_metadata = contact_sites.get_contact_sites_pairwise(
-        cg,
-        np.uint64(first_node_id),
-        np.uint64(second_node_id),
-        end_time=timestamp,
-        exact_location=exact_location,
-    )
-    return contact_sites_list, cs_metadata
-
-
 ### SPLIT PREVIEW --------------------------------------------------------------
 
 

pychunkedgraph/app/segmentation/legacy/routes.py

@@ -164,16 +164,6 @@ def handle_subgraph(table_id, root_id):
     return app_utils.tobinary(subgraph_result)
 
 
-### CONTACT SITES --------------------------------------------------------------
-
-
-@bp.route("/<table_id>/segment/<root_id>/contact_sites", methods=["POST", "GET"])
-@auth_requires_permission("view")
-def handle_contact_sites(table_id, root_id):
-    contact_sites = common.handle_contact_sites(table_id, root_id)
-    return jsonify(contact_sites)
-
-
 ### CHANGE LOG -----------------------------------------------------------------
 
 

pychunkedgraph/app/segmentation/v1/routes.py

@@ -316,41 +316,6 @@ def handle_subgraph(table_id, node_id):
     return jsonify_with_kwargs(resp, int64_as_str=int64_as_str)
 
 
-### CONTACT SITES --------------------------------------------------------------
-
-
-@bp.route("/table/<table_id>/node/<node_id>/contact_sites", methods=["GET"])
-@auth_requires_permission("view")
-@remap_public(edit=False)
-def handle_contact_sites(table_id, node_id):
-    int64_as_str = request.args.get("int64_as_str", default=False, type=toboolean)
-    contact_sites, contact_site_metadata = common.handle_contact_sites(
-        table_id, node_id
-    )
-    resp = {
-        "contact_sites": contact_sites,
-        "contact_site_metadata": contact_site_metadata,
-    }
-    return jsonify_with_kwargs(resp, int64_as_str=int64_as_str)
-
-
-@bp.route(
-    "/table/<table_id>/node/contact_sites_pair/<first_node_id>/<second_node_id>",
-    methods=["GET"],
-)
-@auth_requires_permission("view")
-@remap_public(edit=False)
-def handle_pairwise_contact_sites(table_id, first_node_id, second_node_id):
-    int64_as_str = request.args.get("int64_as_str", default=False, type=toboolean)
-    contact_sites, contact_site_metadata = common.handle_pairwise_contact_sites(
-        table_id, first_node_id, second_node_id
-    )
-    resp = {
-        "contact_sites": contact_sites,
-        "contact_site_metadata": contact_site_metadata,
-    }
-    return jsonify_with_kwargs(resp, int64_as_str=int64_as_str)
-
 
 ### CHANGE LOG -----------------------------------------------------------------
 

pychunkedgraph/backend/__init__.py

@@ -75,14 +75,14 @@ def bigtable_config(self):
 
     @property
     def resolution(self) -> np.ndarray:
-        return np.array(self._ws_cv.resolution)        
+        return np.array(self._ws_cv.resolution)
 
     @property
     def layer_count(self) -> int:
         if self._layer_count:
             return self._layer_count
         bbox = np.array(self._ws_cv.bounds.to_list()).reshape(2, 3)
-        n_chunks = ((bbox[1] - bbox[0]) / self._graph_config.chunk_size).astype(np.int)
+        n_chunks = ((bbox[1] - bbox[0]) / self._graph_config.chunk_size).astype(int)
         self._layer_count = (
             int(np.ceil(log_n(np.max(n_chunks), self._graph_config.fanout))) + 2
         )
@@ -102,7 +102,7 @@ def layer_chunk_bounds(self) -> Dict:
         layer_bounds_d = {}
         for layer in range(2, self.layer_count):
             layer_bounds = chunks_boundary / (2 ** (layer - 2))
-            layer_bounds_d[layer] = np.ceil(layer_bounds).astype(np.int)
+            layer_bounds_d[layer] = np.ceil(layer_bounds).astype(int)
         self._layer_bounds_d = layer_bounds_d
         return self._layer_bounds_d