Merge branch 'master' into groupquery

.github/workflows/main.yml

@@ -0,0 +1,90 @@
+name: h5pyd CI
+
+on:
+  push:
+  pull_request:
+    branches: [master]
+
+env:
+  ADMIN_PASSWORD: admin
+  ADMIN_USERNAME: admin
+  USER_NAME: test_user1
+  USER_PASSWORD: test
+  USER2_NAME: test_user2
+  USER2_PASSWORD: test
+  HSDS_USERNAME: test_user1
+  HSDS_PASSWORD: test
+  HSDS_ENDPOINT: http+unix://%2Ftmp%2Fhs%2Fsn_1.sock
+  ROOT_DIR: ${{github.workspace}}/hsds/hsds_root
+  BUCKET_NAME: hsds_bucket
+  HS_ENDPOINT: http+unix://%2Ftmp%2Fhs%2Fsn_1.sock
+  H5PYD_TEST_FOLDER: /home/test_user1/h5pyd_tests/
+
+jobs:
+  build-and-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest,]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Lint with flake8
+        shell: bash
+        run: |
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --max-complexity=10 --max-line-length=127 --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+
+      - name: Install package
+        shell: bash
+        run: |
+          pip install -e .
+
+      - name: Checkout HSDS 
+        uses: actions/checkout@v3
+        with:
+          repository: HDFGroup/hsds
+          path: ${{github.workspace}}/hsds
+
+      - name: Install HSDS
+        shell: bash
+        run: |
+          cd ${{github.workspace}}/hsds
+          pip install -e .
+
+      - name: Start HSDS
+        shell: bash
+        run: |
+          cd ${{github.workspace}}/hsds
+          mkdir hsds_root
+          mkdir hsds_root/hsds_bucket
+          cp admin/config/groups.default admin/config/groups.txt
+          cp admin/config/passwd.default admin/config/passwd.txt
+          ./runall.sh --no-docker 1 &
+          sleep 11 # let the nodes get ready
+          python tests/integ/setup_test.py
+
+      - name: Create h5pyd test folder
+        shell: bash
+        run: |
+          HS_USERNAME=test_user1 HS_PASSWORD=test TEST2_USERNAME=test_user1 TEST2_PASSWORD=test hstouch -v /home/test_user1/h5pyd_tests/
+
+      - name: Run h5pyd tests
+        shell: bash
+        run: |
+          HS_USERNAME=test_user1 HS_PASSWORD=test TEST2_USERNAME=test_user1 TEST2_PASSWORD=test python testall.py

docs/conf.py

@@ -16,9 +16,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-        'sphinx.ext.intersphinx',
-        'sphinx.ext.extlinks',
-        'sphinx.ext.mathjax',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.extlinks',
+    'sphinx.ext.mathjax',
 ]
 
 # intersphinx_mapping = {'low': ('https://api.h5py.org', None)}

examples/read_example.py

@@ -12,10 +12,12 @@
 
 import h5pyd as h5py
 
+
 def visit_item(name):
     print("visit:", name)
     return None
 
+
 def find_g1_2(name):
     print("visit:", name)
     if name.endswith("g1.2"):
@@ -26,12 +28,13 @@ def visit_item_obj(name, obj):
     print("visit:", name, obj.id.id)
     return None
 
+
 print("version:", h5py.version.version)
 
 # this is the path specified in the "post-install instructions"
 # see:  "Test Data Setup" in:
 #  https://github.com/HDFGroup/hsds/blob/master/docs/post_install.md
-DOMAIN_PATH="/home/test_user1/test/tall.h5"
+DOMAIN_PATH = "/home/test_user1/test/tall.h5"
 print("opening domain:", DOMAIN_PATH)
 
 f = h5py.File(DOMAIN_PATH, "r")
@@ -85,6 +88,3 @@ def visit_item_obj(name, obj):
 
 print("search g1.2:")
 f.visit(find_g1_2)
-
-
-

examples/write_example.py

@@ -25,7 +25,6 @@
 CHUNKS = (1500, 275)
 
 
-
 if len(sys.argv) == 1 or sys.argv[1] in ("-h", "--help"):
     s = f"usage: python {sys.argv[0]} "
     s += "[--ncols=n] "
@@ -138,4 +137,4 @@
 else:
     print("passed!")
 
-f.close()
+f.close()

h5pyd/__init__.py

@@ -34,12 +34,12 @@
 
 
 __doc__ = \
-"""
+    """
     This is the h5pyd package, a Python interface to the HDF REST Server.
 
     Version %s
 
-""" % (version.version)
+    """ % (version.version)
 
 
 def enable_ipython_completer():

h5pyd/_apps/config.py

@@ -38,7 +38,7 @@
         "flags": ["--api_key",],
         "help": "user api key",
         "choices": ["API_KEY"]
-    }, 
+    },
     "hs_bucket": {
         "default": None,
         "flags": ["--bucket",],
@@ -67,11 +67,12 @@
         "default": False,
         "flags": ["--ignore",],
         "help": "don't exit on error"
-    } 
+    }
 }
 
 hscmds = ("hsinfo", "hsconfigure", "hsls", "hstouch", "hsload", "hsget", "hsacl", "hsrm", "hsdiff")
 
+
 class Config:
     """
     User Config state
@@ -163,7 +164,7 @@ def setitem(self, name, value, flags=None, choices=None, help=None):
         """ Set a config item """
         if name not in self._names:
             self._names.append(name)
-        self._values[name] = value 
+        self._values[name] = value
         if flags is not None:
             self._flags[name] = flags
             for flag in flags:
@@ -175,7 +176,7 @@ def setitem(self, name, value, flags=None, choices=None, help=None):
 
     def __setitem__(self, name, value):
         self.setitem(name, value)
-     
+
     def __len__(self):
         return len(self._names)
 
@@ -212,35 +213,33 @@ def get_see_also(self, this_cmd):
                 msg += f"{cmd}, "
         msg = msg[:-2]  # remove trailing comma
         return msg
-
 
     def get_help_message(self, name):
-        help_text= self.get_help(name)
+        help_text = self.get_help(name)
         flags = self.get_flags(name)
         choices = self.get_choices(name)
         if not help_text or len(flags) == 0:
             return None
-        
+
         msg = flags[0]
         for i in range(1, len(flags)):
             msg += f", {flags[i]}"
         if choices:
             if len(choices) == 1:
                 msg += f" {choices[0]}"
             else:
-                msg += " {" 
+                msg += " {"
                 for choice in choices:
                     msg += f"{choice}|"
                 msg = msg[:-1]
                 msg += "}"
         if len(msg) < 40:
-            pad = " "*(40 - len(msg))
+            pad = " " * (40 - len(msg))
             msg += pad
-        
+
         msg += f" {help_text}"
-        
+
         return msg
-
 
     def get_nargs(self, name):
         choices = self._choices.get(name)
@@ -260,15 +259,15 @@ def get_names(self):
 
     def set_cmd_flags(self, args, allow_post_flags=False):
         """ process any command line options
-            return any place argument as a list 
+            return any place argument as a list
         """
         options = []
         argn = 0
         while argn < len(args):
             arg = args[argn]
             val = None
             if len(args) > argn + 1:
-                val = args[argn+1]
+                val = args[argn + 1]
             if not arg.startswith("-"):
                 options.append(arg)
                 argn += 1
@@ -299,7 +298,7 @@ def set_cmd_flags(self, args, allow_post_flags=False):
                     self._values[name] = val
                     argn += 2
         return options
-    
+
     def get_loglevel(self):
         val = self._values["loglevel"]
         val = val.upper()
@@ -329,13 +328,3 @@ def print(self, msg):
             logging.info(msg)
         if self._values.get("verbose"):
             print(msg)
-
-
-
-
-
-
-
-
-
-