Merge pull request #348 from ericmjl/bump_up_actions

bump up actions

.github/workflows/check.yaml

@@ -7,12 +7,12 @@ on:
 jobs:
   # Check that source code is black-ified
   black:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Checkout repository
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Setup Python
         with:
           python-version: 3.9
@@ -28,9 +28,9 @@ jobs:
 
   # This job is copied over from `deploy.yaml`
   build-environment:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # See: https://github.com/marketplace/actions/setup-conda
       - uses: s-weigand/setup-conda@v1
@@ -40,7 +40,7 @@ jobs:
       # Build cache of environment
       - name: Cache conda environment
         id: cache-environment
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         # Conda environment build step depends on two files,
         # so we ensure that the hash key contains both their hashes.
         with:
@@ -54,21 +54,21 @@ jobs:
 
       # See: https://github.com/actions/upload-artifact
       - name: Upload environment
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nams-tarball
           path: nams.tar.gz
 
   # This job is copied over from `deploy.yaml`
   build-deploy-website:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     needs: build-environment
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # https://github.com/actions/download-artifact
       - name: Download environment tarball
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: nams-tarball
 
@@ -78,7 +78,7 @@ jobs:
       # Build cache of website
       - name: Cache website
         id: cache-website
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         # Website build step depends on the following files:
         # - mkdocs.yml
         # - scripts/ci/build_website.sh
@@ -105,13 +105,13 @@ jobs:
 
   # This job is copied over from `deploy.yaml`
   build-deploy-leanpub:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     needs: build-environment
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Download environment tarball
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: nams-tarball
 
@@ -121,7 +121,7 @@ jobs:
       # Build cache of leanpub source
       - name: Cache LeanPub
         id: cache-leanpub
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         # Leanpub build step depends on the following files:
         # - scripts/bookbuilder
         # - scripts/ci/build_website.sh

.github/workflows/deploy.yaml

@@ -13,9 +13,9 @@ on:
 
 jobs:
   build-environment:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # See: https://github.com/marketplace/actions/setup-conda
       - uses: s-weigand/setup-conda@v1
@@ -25,7 +25,7 @@ jobs:
       # Build cache of environment
       - name: Cache conda environment
         id: cache-environment
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         # Conda environment build step depends on two files,
         # so we ensure that the hash key contains both their hashes.
         with:
@@ -39,20 +39,20 @@ jobs:
 
       # See: https://github.com/actions/upload-artifact
       - name: Upload environment
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nams-tarball
           path: nams.tar.gz
 
   build-deploy-website:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     needs: build-environment
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # https://github.com/actions/download-artifact
       - name: Download environment tarball
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: nams-tarball
 
@@ -77,13 +77,13 @@ jobs:
           disable_nojekyll: false
 
   build-deploy-leanpub:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     needs: build-environment
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Download environment tarball
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: nams-tarball
 

environment.yml

@@ -30,7 +30,6 @@ dependencies:
   - pymdown-extensions
   - pyprojroot
   - python-louvain
-  - rise
   - scipy
   - seaborn
   - tabulate  # used for exporting dataframe as Markdown tables

nams/solutions/got.py

@@ -15,7 +15,7 @@ def weighted_degree(G, weight):
 def correlation_centrality(G):
     cor = pd.DataFrame.from_records(
         [
-            nx.pagerank_numpy(G, weight="weight"),
+            nx.pagerank(G, weight="weight"),
             nx.betweenness_centrality(G, weight="weight_inv"),
             weighted_degree(G, "weight"),
             nx.degree_centrality(G),

notebooks/03-practical/01-io.ipynb

@@ -318,7 +318,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(nx.info(G))"
+    "print(G)"
    ]
   },
   {
@@ -531,11 +531,6 @@
     "\n",
     "Since NetworkX graphs are Python objects,\n",
     "the canonical way to save them is by pickling them.\n",
-    "You can do this using:\n",
-    "\n",
-    "```python\n",
-    "nx.write_gpickle(G, file_path)\n",
-    "```\n",
     "\n",
     "Here's an example in action:"
    ]
@@ -546,7 +541,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nx.write_gpickle(G, \"/tmp/divvy.pkl\")"
+    "import pickle\n",
+    "with open(\"/tmp/divvy.pkl\", \"wb\") as f:\n",
+    "    pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)"
    ]
   },
   {
@@ -562,7 +559,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "G_loaded = nx.read_gpickle(\"/tmp/divvy.pkl\")"
+    "with open(\"/tmp/divvy.pkl\", \"rb\") as f:\n",
+    "    G_loaded = pickle.load(f)"
    ]
   },
   {

notebooks/05-casestudies/01-gameofthrones.ipynb

@@ -391,7 +391,7 @@
    "source": [
     "# by default weight attribute in PageRank is weight\n",
     "# so we use weight=None to find the unweighted results\n",
-    "sorted(nx.pagerank_numpy(graphs[0],\n",
+    "sorted(nx.pagerank(graphs[0],\n",
     "        weight=None).items(),\n",
     "        key=lambda x:x[1], reverse=True)[0:10]"
    ]
@@ -402,7 +402,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sorted(nx.pagerank_numpy(\n",
+    "sorted(nx.pagerank(\n",
     "    graphs[0], weight='weight').items(),\n",
     "    key=lambda x:x[1], reverse=True)[0:10]"
    ]

notebooks/05-casestudies/02-airport.ipynb

@@ -298,7 +298,7 @@
     "# Number of nodes = airports\n",
     "# Number of edges = routes\n",
     "\n",
-    "print(nx.info(pass_2015_network))"
+    "print(pass_2015_network)"
    ]
   },
   {
@@ -1354,7 +1354,7 @@
    "source": [
     "# number of nodes -> airports\n",
     "# number of edges -> routes\n",
-    "print(nx.info(united_network))"
+    "print(united_network)"
    ]
   },
   {

scripts/ci/build_environment.sh

@@ -1,6 +1,7 @@
 # Build conda environment.
+conda update -n base -c defaults conda
 conda install -c conda-forge mamba
-conda env create -f environment.yml
+mamba env create -f environment.yml
 conda activate nams || source activate nams
 python -m pip install --no-deps git+https://github.com/greenape/mknotebooks.git
 python -m pip install --no-deps .