Merge pull request #122 from echemdata/ml-evs/fix-ci

Pin and update release downloader action

.github/workflows/ci.yml

@@ -26,11 +26,28 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-      - name: Cached LFS checkout
-        uses: nschloe/action-cached-lfs-checkout@v1.2.2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          enableCrossOsArchive: true
+          lfs: false
+
+      # Due to limited LFS bandwidth, it is preferable to download
+      # test files from the last release.
+      #
+      # This does mean that testing new LFS files in the CI is tricky;
+      # care should be taken to also test new files locally first
+      # Tests missing these files in the CI should still fail.
+      - name: Download static files from last release for testing
+        uses: robinraju/release-downloader@v1.12
+        with:
+          latest: true
+          tarBall: true
+          out-file-path: /home/runner/work/last-release
+          extract: true
+
+      - name: Copy test files from static downloaded release
+        run: |
+          cp -r /home/runner/work/last-release/*/tests/testdata tests
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -50,5 +67,5 @@ jobs:
           tox -vv --notest
 
       - name: Run all tests
-        run: |
+        run: |-
           tox --skip-pkg-install

README.md

@@ -47,14 +47,30 @@ The latest galvani releases can be installed from [PyPI](https://pypi.org/projec
 pip install galvani
 ```
 
-The latest development version can be installed with `pip` directly from GitHub:
+The latest development version can be installed with `pip` directly from GitHub (see note about git-lfs below):
 
 ```shell
-pip install git+https://github.com/echemdata/galvani
+GIT_LFS_SKIP_SMUDGE=1 pip install git+https://github.com/echemdata/galvani
 ```
 
 ## Development installation and contributing 
 
+> [!WARNING]
+> 
+> This project uses Git Large File Storage (LFS) to store its test files,
+> however the LFS quota provided by GitHub is frequently exceeded. 
+> This means that anyone cloning the repository with LFS installed will get
+> failures unless they set the `GIT_LFS_SKIP_SMUDGE=1` environment variable when
+> cloning. 
+> The full test data from the last release can always be obtained by
+> downloading the GitHub release archives (tar or zip), at
+> https://github.com/echemdata/galvani/releases/latest
+>
+> If you wish to add test files, please ensure they are as small as possible,
+> and take care that your tests work locally without the need for the LFS files.
+> Ideally, you could commit them to your fork when making a PR, and then they
+> can be converted to LFS files as part of the review.
+
 If you wish to contribute to galvani, please clone the repository and install the testing dependencies:
 
 ```shell

galvani/BioLogic.py

@@ -56,7 +56,7 @@ def fieldname_to_dtype(fieldname):
         "|Permittivity|",
         "Tan(Delta)",
     ):
-        return (fieldname, np.float_)
+        return (fieldname, np.float64)
     elif fieldname in (
         "Q charge/discharge/mA.h",
         "step time/s",
@@ -66,15 +66,15 @@ def fieldname_to_dtype(fieldname):
         "Efficiency/%",
         "Capacity/mA.h",
     ):
-        return (fieldname, np.float_)
+        return (fieldname, np.float64)
     elif fieldname in ("cycle number", "I Range", "Ns", "half cycle", "z cycle"):
         return (fieldname, np.int_)
     elif fieldname in ("dq/mA.h", "dQ/mA.h"):
-        return ("dQ/mA.h", np.float_)
+        return ("dQ/mA.h", np.float64)
     elif fieldname in ("I/mA", "<I>/mA"):
-        return ("I/mA", np.float_)
+        return ("I/mA", np.float64)
     elif fieldname in ("Ewe/V", "<Ewe>/V", "Ecell/V", "<Ewe/V>"):
-        return ("Ewe/V", np.float_)
+        return ("Ewe/V", np.float64)
     elif fieldname.endswith(
         (
             "/s",
@@ -103,7 +103,7 @@ def fieldname_to_dtype(fieldname):
             "/%",
         )
     ):
-        return (fieldname, np.float_)
+        return (fieldname, np.float64)
     else:
         raise ValueError("Invalid column header: %s" % fieldname)
 
@@ -276,7 +276,7 @@ VMPdata_colID_dtype_map = {
     11: ("<I>/mA", "<f8"),
     13: ("(Q-Qo)/mA.h", "<f8"),
     16: ("Analog IN 1/V", "<f4"),
-    17: ("Analog IN 2/V", "<f4"),  # Probably column 18 is Analog IN 3/V, if anyone hits this error in the future
+    17: ("Analog IN 2/V", "<f4"),  # Probably column 18 is Analog IN 3/V, if anyone hits this error in the future  # noqa: E501
     19: ("control/V", "<f4"),
     20: ("control/mA", "<f4"),
     23: ("dQ/mA.h", "<f8"),  # Same as 7?

galvani/res2sqlite.py

@@ -571,13 +571,25 @@ def mdb_get_version(filename):
     return version_tuple
 
 
-def convert_arbin_to_sqlite(input_file, output_file):
+def convert_arbin_to_sqlite(input_file, output_file=None):
     """Read data from an Arbin .res data file and write to a sqlite file.
 
-    Any data currently in the sqlite file will be erased!
+    Any data currently in an sqlite file at `output_file` will be erased!
+
+    Parameters:
+        input_file (str): The path to the Arbin .res file to read from.
+        output_file (str or None): The path to the sqlite file to write to; if None,
+            return a `sqlite3.Connection` into an in-memory database.
+
+    Returns:
+        None or sqlite3.Connection
+
     """
     arbin_version = mdb_get_version(input_file)
 
+    if output_file is None:
+        output_file = ":memory:"
+
     s3db = sqlite3.connect(output_file)
 
     tables_to_convert = copy(mdb_tables)
@@ -602,6 +614,11 @@ def convert_arbin_to_sqlite(input_file, output_file):
     print("Vacuuming database...")
     s3db.executescript("VACUUM; ANALYZE;")
 
+    if output_file == ":memory:":
+        return s3db
+
+    s3db.close()
+
 
 def main(argv=None):
     parser = argparse.ArgumentParser(

setup.py

@@ -12,7 +12,7 @@ with open(os.path.join(os.path.dirname(__file__), "README.md")) as f:
 
 setup(
     name="galvani",
-    version="0.3.0",
+    version="0.4.1",
     description="Open and process battery charger log data files",
     long_description=readme,
     long_description_content_type="text/markdown",

tests/test_Arbin.py

@@ -53,6 +53,16 @@ def test_convert_Arbin_to_sqlite_function(testdata_dir, tmpdir, basename):
         csr.fetchone()
 
 
+@pytest.mark.parametrize("basename", ["arbin1", "UM34_Test005E"])
+def test_convert_Arbin_to_sqlite_function_in_memory(testdata_dir, tmpdir, basename):
+    """Convert an Arbin file to an in-memory SQLite database."""
+    res_file = os.path.join(testdata_dir, basename + ".res")
+    conn = None
+    with res2sqlite.convert_arbin_to_sqlite(res_file) as conn:
+        csr = conn.execute("SELECT * FROM Channel_Normal_Table;")
+        csr.fetchone()
+
+
 @pytest.mark.skipif(
     not have_mdbtools, reason="Reading the Arbin file requires MDBTools"
 )