Bump urllib3 from 2.5.0 to 2.6.3 in /docs

.github/workflows/darshan-3.4.2.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     timeout-minutes: 20
 
@@ -41,7 +41,7 @@ jobs:
       - name: Build Darshan
         run: |
           cd darshan
-          git checkout darshan-3.4.0
+          git checkout darshan-3.4.2
           bash prepare.sh
           cd darshan-util
           ./configure
@@ -57,7 +57,7 @@ jobs:
         run: |
           python -m ensurepip --upgrade
           pip install --upgrade setuptools
-          pip install darshan==3.4.0.1
+          pip install darshan==3.4.2
           pip install -r requirements.txt
           pip install .
 
@@ -125,10 +125,6 @@ jobs:
         run: |
           dxt-explorer --debug --start 3.7 --end 3.9 --from 1 --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
 
-      - name: Setup upterm session
-        if: ${{ failure() }}
-        uses: owenthereal/action-upterm@v1
-
       - name: Upload Artifact
         if: always()
         uses: actions/upload-artifact@v4

.github/workflows/darshan-3.4.4.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     timeout-minutes: 20
 
@@ -125,10 +125,6 @@ jobs:
         run: |
           dxt-explorer --debug --start 3.7 --end 3.9 --from 1 --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
 
-      - name: Setup upterm session
-        if: ${{ failure() }}
-        uses: owenthereal/action-upterm@v1
-
       - name: Upload Artifact
         if: always()
         uses: actions/upload-artifact@v4

.github/workflows/darshan-3.4.6.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     timeout-minutes: 20
 
@@ -125,10 +125,6 @@ jobs:
         run: |
           dxt-explorer --debug --start 3.7 --end 3.9 --from 1 --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
 
-      - name: Setup upterm session
-        if: ${{ failure() }}
-        uses: owenthereal/action-upterm@v1
-
       - name: Upload Artifact
         if: always()
         uses: actions/upload-artifact@v4

.github/workflows/darshan-3.4.7.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     timeout-minutes: 20
 
@@ -125,10 +125,6 @@ jobs:
         run: |
           dxt-explorer --debug --start 3.7 --end 3.9 --from 1 --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
 
-      - name: Setup upterm session
-        if: ${{ failure() }}
-        uses: owenthereal/action-upterm@v1
-
       - name: Upload Artifact
         if: always()
         uses: actions/upload-artifact@v4

.github/workflows/darshan-3.5.0.yml

@@ -0,0 +1,136 @@
+name: DXT Explorer (Darshan 3.5.0)
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  explorer:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
+    timeout-minutes: 20
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Dependencies
+        run: |
+          git clone https://github.com/darshan-hpc/darshan.git
+
+      - name: Install macOS Dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install libtool autoconf automake
+
+      - name: Build Darshan
+        run: |
+          cd darshan
+          git checkout 3.5.0
+          bash prepare.sh
+          cd darshan-util
+          ./configure
+          make
+          sudo make install
+
+      - name: Configure Linux
+        if: runner.os == 'Linux'
+        run: |
+          sudo ldconfig
+
+      - name: Install DXT Explorer
+        run: |
+          python -m ensurepip --upgrade
+          pip install --upgrade setuptools
+          pip install darshan==3.5.0
+          pip install -r requirements.txt
+          pip install .
+
+      - name: Run DXT Explorer (help)
+        run: |
+          dxt-explorer -h
+
+      - name: Run DXT Explorer (list)
+        run: |
+          dxt-explorer --debug --list sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (operation)
+        run: |
+          dxt-explorer --debug sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (transfer)
+        run: |
+          dxt-explorer --debug --transfer sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan 
+
+      - name: Run DXT Explorer (spatiality)
+        run: |
+          dxt-explorer --debug --spatiality sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (io phase)
+        run: |
+          dxt-explorer --debug --io_phase sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (ost usage operation)
+        run: |
+          dxt-explorer --debug --ost_usage_operation sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (ost usage transfer)
+        run: |
+          dxt-explorer --debug --ost_usage_transfer sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (rank zero workload)
+        run: |
+          dxt-explorer --debug --rank_zero_workload sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (unbalanced workload)
+        run: |
+          dxt-explorer --debug --unbalanced_workload sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (stragglers)
+        run: |
+          dxt-explorer --debug --stragglers sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (truncate runtime)
+        run: |
+          dxt-explorer --debug --start 3.7 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (truncate runtime)
+        run: |
+          dxt-explorer --debug --end 3.9 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (truncate rank)
+        run: |
+          dxt-explorer --debug --from 1 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (truncate rank)
+        run: |
+          dxt-explorer --debug --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Run DXT Explorer (truncate both)
+        run: |
+          dxt-explorer --debug --start 3.7 --end 3.9 --from 1 --to 100 sample/jeanbez_8_benchmark_parallel_id45195555_8-6-50011-11681279140261054765_1628283217.darshan
+
+      - name: Upload Artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: tests-${{ matrix.os }}-${{ matrix.python-version }}
+          path: sample/**
+          retention-days: 1
+
+

docs/requirements.txt

@@ -8,4 +8,4 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 sphinxemoji==0.3.1
-urllib3==2.5.0
+urllib3==2.6.3

explorer/dxt.py

@@ -30,12 +30,12 @@
 import subprocess
 import webbrowser
 import pandas as pd
-import pkg_resources
 import pyranges as pr
 import logging.handlers
 import pyarrow.feather as feather
 # import darshan.backend.cffi_backend as darshanll
 
+from importlib import resources
 from explorer import version as dxt_version
 from packaging import version
 
@@ -298,7 +298,7 @@ def create_dataframe(
                 temp_result["end"] = temp_result["end"].round(decimals=4)
 
                 temp_result.index.name = "segment"
-                temp_result.reset_index(inplace=True)
+                temp_result = temp_result.reset_index()
                 temp_result = temp_result.reindex(columns=column_names)
 
                 df.append(temp_result)
@@ -327,7 +327,7 @@ def create_dataframe(
                 temp_result["end"] = temp_result["end"].round(decimals=4)
 
                 temp_result.index.name = "segment"
-                temp_result.reset_index(inplace=True)
+                temp_result = temp_result.reset_index()
                 temp_result = temp_result.reindex(columns=column_names)
 
                 df.append(temp_result)
@@ -422,8 +422,8 @@ def merge_overlapping_io_phases(self, overlapping_df, df, module):
             ]
         )
 
-        overlapping_df_end = overlapping_df[["End"]].to_numpy()
-        overlapping_df_start = overlapping_df[["Start"]].to_numpy()
+        overlapping_df_end = overlapping_df["End"].to_numpy()
+        overlapping_df_start = overlapping_df["Start"].to_numpy()
         interval_duration = 0
 
         for i in range(len(overlapping_df_end) - 1):
@@ -513,7 +513,8 @@ def merge_overlapping_io_phases(self, overlapping_df, df, module):
                     threshold,
                 ]
 
-        io_phases_df.dropna(inplace=True)
+        io_phases_df = io_phases_df.dropna()
+
         return io_phases_df
 
     def calculate_io_phases(
@@ -730,7 +731,7 @@ def generate_plot(self, file, report):
                                 self.prefix, file_id, "snapshot", snapshot, "operation"
                             )
                             path = "plots/operation.py"
-                            script = pkg_resources.resource_filename(__name__, path)
+                            script = str(resources.files(__package__ or __name__).joinpath(path))
 
                             command = "python3 {} -f {}.{}.{}-{}.dxt -i {}.{}.{}-{}.io_phases {} {} -o {} -x {} -t {} -r {}".format(
                                 script,
@@ -792,7 +793,7 @@ def generate_plot(self, file, report):
                         self.prefix, file_id, "operation"
                     )
                     path = "plots/operation.py"
-                    script = pkg_resources.resource_filename(__name__, path)
+                    script = str(resources.files(__package__ or __name__).joinpath(path))
 
                     command = "python3 {} -f {}.{}.dxt -i {}.{}.io_phases{} {} -o {} -x {}".format(
                         script,
@@ -864,7 +865,7 @@ def generate_transfer_plot(self, file, report):
                 output_file = "{}/{}-{}.html".format(self.prefix, file_id, "transfer")
 
                 path = "plots/transfer.py"
-                script = pkg_resources.resource_filename(__name__, path)
+                script = str(resources.files(__package__ or __name__).joinpath(path))
 
                 command = "python3 {} -f {}.{}.dxt {} -o {} -x {}".format(
                     script, file, file_id, limits, output_file, file_name
@@ -912,7 +913,7 @@ def generate_spatiality_plot(self, file, report):
                 output_file = "{}/{}-{}.html".format(self.prefix, file_id, "spatiality")
 
                 path = "plots/spatiality.py"
-                script = pkg_resources.resource_filename(__name__, path)
+                script = str(resources.files(__package__ or __name__).joinpath(path))
 
                 command = "python3 {} -f {}.{}.dxt -o {} -x {}".format(
                     script, file, file_id, output_file, file_name
@@ -959,7 +960,7 @@ def generate_phase_plot(self, file, report):
             for file_id, file_name in file_ids.items():
                 output_file = "{}/{}-{}.html".format(self.prefix, file_id, "io_phase")
                 path = "plots/io_phase.py"
-                script = pkg_resources.resource_filename(__name__, path)
+                script = str(resources.files(__package__ or __name__).joinpath(path))
 
                 command = "python3 {} -f {}.{}.io_phases -o {} -x {}".format(
                     script, file, file_id, output_file, file_name
@@ -1007,7 +1008,7 @@ def generate_ost_usage_operation_plot(self, file, report):
                     self.prefix, file_id, "ost_usage_operation"
                 )
                 path = "plots/ost_usage_operation.py"
-                script = pkg_resources.resource_filename(__name__, path)
+                script = str(resources.files(__package__ or __name__).joinpath(path))
 
                 command = "python3 {} -f {}.{}.dxt -o {} -x {}".format(
                     script, file, file_id, output_file, file_name
@@ -1057,7 +1058,7 @@ def generate_ost_usage_transfer_plot(self, file, report):
                     self.prefix, file_id, "ost_usage_transfer"
                 )
                 path = "plots/ost_usage_transfer.py"
-                script = pkg_resources.resource_filename(__name__, path)
+                script = str(resources.files(__package__ or __name__).joinpath(path))
 
                 command = "python3 {} -f {}.{}.dxt -o {} -x {}".format(
                     script, file, file_id, output_file, file_name