Merge branch 'main' into 290-docs-constraints

.github/workflows/conda_unit_test.yml

@@ -30,7 +30,7 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Create Python ${{ matrix.python-version }} environment
       uses: mamba-org/setup-micromamba@v1

.github/workflows/publish-docs.yml

@@ -54,16 +54,21 @@ jobs:
       run: |
         echo "The docs will be published from this workflow run."
 
-    - name: Install Python ${{ matrix.python-version }} Conda environment with micromamba from env-dev.yml
-      uses: mamba-org/provision-with-micromamba@main
+    - name: Create Python documentation environment
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: env-dev.yml
-        environment-name: test
+        environment-name: documentation
+        condarc: |
+          channel-priority: flexible
+        init-shell: bash
+        cache-environment: true
+        cache-environment-key: env-key
 
     - name: Install the package locally
       shell: bash -l {0}
       run: |
-        pip install -e .
+        pip install --no-deps -e . -vv
 
     - name: Diagnostics
       shell: bash -l {0}
@@ -72,7 +77,7 @@ jobs:
         conda list
         env | sort | grep -i CONDA
 
-    - name: Build Docs
+    - name: Build Docs with Sphinx
       shell: bash -l {0}
       run: |
         make -C docs clean html

RELEASE_NOTES.rst

@@ -30,6 +30,7 @@ New Features and/or Enhancements
 * Add ``SoleilNanoscopiumRobot`` diffractometer geometry.
 * Add ``SoleilSixsMed2p3v2`` diffractometer geometry.
 * Export and restore diffractometer configuration as JSON string, YAML string, Python dictionary, or file.
+* Add ``user.current_diffractometer()`` function.
 
 Fixes
 -----

env-dev.yml

@@ -16,7 +16,7 @@ dependencies:
   - apischema
   - black
   - bluesky
-  - databroker =1.2
+  - databroker
   - flake8
   - hkl
   - ipython

environment.yml

@@ -15,7 +15,6 @@ dependencies:
   - python >=3.8,<3.12
   - apischema
   - bluesky
-  - databroker =1.2
   - hkl
   - numpy
   - ophyd

hkl/configuration.py

@@ -53,6 +53,8 @@
 DEFAULT_WAVELENGTH = 1.54  # angstrom
 EXPORT_FORMATS = "dict json yaml".split()
 
+EQUAL_TOLERANCE = 1.0e-7
+
 
 # standard value checks, raise exception(s) when appropriate
 def _check_key(key, biblio, intro):
@@ -261,12 +263,12 @@ def validate(self, dc_obj):
 
     def write(self, diffractometer):
         """Write sample details to diffractometer."""
-        s = diffractometer.calc._samples.get(self.name)
+        sample = diffractometer.calc._samples.get(self.name)
         lattice_parameters = list(self.lattice.values)
-        if s is None:
-            s = diffractometer.calc.new_sample(self.name, lattice=lattice_parameters)
+        if sample is None:
+            sample = diffractometer.calc.new_sample(self.name, lattice=lattice_parameters)
         else:
-            s.lattice = lattice_parameters
+            sample.lattice = lattice_parameters
 
         reflection_list = []
         for reflection in self.reflections:
@@ -282,18 +284,18 @@ def write(self, diffractometer):
             w1 = rdict["wavelength"]
             try:
                 diffractometer.calc.wavelength = w1
-                r = diffractometer.calc.sample.add_reflection(*args)
+                r = sample.add_reflection(*args)
+                if rdict["orientation_reflection"]:
+                    reflection_list.append(r)
             except RuntimeError as exc:
                 raise RuntimeError(f"could not add reflection({args}, wavelength={w1})") from exc
             finally:
                 diffractometer.calc.wavelength = w0
-
-            if rdict["orientation_reflection"]:
-                reflection_list.append(r)
+            # Remaining code will not be executed if exception was raised.
 
             if len(reflection_list) > 1:
                 r1, r2 = reflection_list[0], reflection_list[1]
-                diffractometer.calc.sample.compute_UB(r1, r2)
+                sample.compute_UB(r1, r2)
 
 
 @dataclass
@@ -550,6 +552,11 @@ def restore(self, data, clear=True, restore_constraints=True):
             If ``True`` (default), remove any previous configuration of the
             diffractometer and reset it to default values before restoring the
             configuration.
+
+            If ``False``, sample reflections will be append with all reflections
+            included in the configuration data for that sample.  Existing
+            reflections will not be changed.  The user may need to edit the
+            list of reflections after ``restore(clear=False)``.
         restore_constraints *bool*:
             If ``True`` (default), restore any constraints provided.
 

hkl/sample.py

@@ -1,3 +1,5 @@
+"""Sample on the diffractometer."""
+
 import logging
 
 import numpy as np
@@ -88,21 +90,19 @@ class HklSample(object):
 
     .. autosummary::
 
+        ~name
         ~add_reflection
-        ~affine
+        ~remove_reflection
+        ~swap_orientation_reflections
         ~clear_reflections
+        ~affine
         ~compute_UB
-        ~hkl_calc
-        ~hkl_sample
         ~lattice
-        ~name
         ~reciprocal
         ~reflection_measured_angles
         ~reflection_theoretical_angles
         ~reflections
         ~reflections_details
-        ~remove_reflection
-        ~swap_orientation_reflections
         ~U
         ~UB
         ~ux
@@ -113,6 +113,8 @@ class HklSample(object):
 
     .. autosummary::
 
+        ~hkl_calc
+        ~hkl_sample
         ~__repr__
         ~__str__
         ~_create_reflection

hkl/tests/__init__.py

@@ -1,32 +0,0 @@
-import logging
-
-import numpy
-
-from ..util import new_lattice
-
-logger = logging.getLogger("ophyd_session_test")
-
-TARDIS_TEST_MODE = "lifting_detector_mu"
-TWO_PI = 2 * numpy.pi
-
-
-def new_sample(diffractometer, name, lattice):
-    diffractometer.calc.new_sample(name, lattice=lattice)
-
-
-def sample_kryptonite(diffractometer):
-    triclinic = new_lattice(4, 5, 6, 75, 85, 95)
-    new_sample(diffractometer, "kryptonite", lattice=triclinic)
-
-
-def sample_silicon(diffractometer):
-    from .. import SI_LATTICE_PARAMETER
-
-    cubic = new_lattice(SI_LATTICE_PARAMETER)
-    new_sample(diffractometer, "silicon", lattice=cubic)
-
-
-def sample_vibranium(diffractometer):
-    a0 = TWO_PI
-    cubic = new_lattice(a0)
-    new_sample(diffractometer, "vibranium", lattice=cubic)

hkl/tests/test_configuration.py

@@ -15,7 +15,7 @@
 from ..configuration import DCSample
 from ..util import Constraint
 from ..util import new_lattice
-from . import TWO_PI
+from .tools import TWO_PI
 
 TEST_CONFIG_FILE = "data/e4c-config.json"
 

hkl/tests/test_restore_reflections.py

@@ -0,0 +1,61 @@
+"""
+Test that reflections from one sample are not restored to other samples.
+"""
+
+from .. import DiffractometerConfiguration
+from .tools import sample_kryptonite
+from .tools import sample_silicon
+from .tools import sample_vibranium
+
+
+def test_issue289(e4cv):
+    assert e4cv is not None
+
+    # setup four samples with reflections, all of them different
+    main = e4cv.calc.sample  # the default sample
+    assert len(main.reflections) == 0
+    m_100 = main.add_reflection(1, 0, 0, (-45, 0, 0, 0))
+    m_010 = main.add_reflection(0, 1, 0, (45, 0, 0, 0))
+    main.compute_UB(m_100, m_010)
+
+    kryptonite = sample_kryptonite(e4cv)
+    assert len(kryptonite.reflections) == 0
+    k_200 = kryptonite.add_reflection(2, 0, 0, (30, 0, 10, 60))
+    k_020 = kryptonite.add_reflection(0, 2, 0, (30, 90, 10, 60))
+    kryptonite.compute_UB(k_200, k_020)
+
+    vibranium = sample_vibranium(e4cv)
+    assert len(vibranium.reflections) == 0
+    v_003 = vibranium.add_reflection(0, 0, 3, (20.33, 4.33, 8.33, 40.33))
+    v_033 = vibranium.add_reflection(0, 3, 3, (20.33, -94.33, 8.33, 40.33))
+    vibranium.compute_UB(v_003, v_033)
+
+    silicon = sample_silicon(e4cv)
+    assert len(silicon.reflections) == 0
+    s_440 = silicon.add_reflection(4, 4, 0, (34, 44, 54, 64))
+    s_444 = silicon.add_reflection(4, 4, 4, (34, 134, 54, 64))
+    silicon.compute_UB(s_440, s_444)
+
+    n_saved_reflections = 2
+    assert len(main.reflections) == n_saved_reflections
+    assert len(kryptonite.reflections) == n_saved_reflections
+    assert len(silicon.reflections) == n_saved_reflections
+    assert len(vibranium.reflections) == n_saved_reflections
+    # same test, using diffractometer sample dictionary now.
+    for sample in e4cv.calc._samples.values():
+        assert len(sample.reflections) == n_saved_reflections, f"{sample.name=}"
+    assert len(e4cv.calc._samples) == 4
+
+    agent = DiffractometerConfiguration(e4cv)
+    assert agent is not None
+    config = agent.export()
+    assert isinstance(config, str)
+
+    # Restore the configuration without clearing the diffractometer first.
+    # This should not change the number of samples or the number of
+    # reflections for any of the samples.
+    agent.restore(config, clear=False)
+
+    assert len(e4cv.calc._samples) == 4
+    for sample in e4cv.calc._samples.values():
+        assert len(sample.reflections) == 2 * n_saved_reflections

hkl/tests/test_tardis.py

@@ -9,7 +9,7 @@
 
 @pytest.fixture(scope="function")
 def kcf_sample(tardis):
-    from . import new_sample
+    from .tools import new_sample
 
     # note: orientation matrix (below) was pre-computed with this wavelength
     # wavelength units must match lattice unit cell length units
@@ -90,7 +90,7 @@ def test_params(tardis):
     """
     Make sure the parameters are set correctly
     """
-    from . import TARDIS_TEST_MODE
+    from .tools import TARDIS_TEST_MODE
 
     calc = tardis.calc
     assert calc.pseudo_axis_names == "h k l".split()
@@ -319,7 +319,7 @@ def test_sample1(sample1, tardis):
 
 def test_sample1_calc_only():
     """Comparisons start with the Tardis' calc support (no Diffractometer object)."""
-    from . import TARDIS_TEST_MODE
+    from .tools import TARDIS_TEST_MODE
 
     tardis_calc = hkl_calc.CalcE6C()
 

hkl/tests/tools.py

@@ -0,0 +1,38 @@
+"""
+Common code, setups, constants, ... for these tests.
+
+Avoids direct imports of __init__.py.
+"""
+
+import logging
+
+import numpy
+
+from ..util import new_lattice
+
+logger = logging.getLogger("ophyd_session_test")
+
+TARDIS_TEST_MODE = "lifting_detector_mu"
+TWO_PI = 2 * numpy.pi
+
+
+def new_sample(diffractometer, name, lattice):
+    return diffractometer.calc.new_sample(name, lattice=lattice)
+
+
+def sample_kryptonite(diffractometer):
+    triclinic = new_lattice(4, 5, 6, 75, 85, 95)
+    return new_sample(diffractometer, "kryptonite", lattice=triclinic)
+
+
+def sample_silicon(diffractometer):
+    from .. import SI_LATTICE_PARAMETER
+
+    cubic = new_lattice(SI_LATTICE_PARAMETER)
+    return new_sample(diffractometer, "silicon", lattice=cubic)
+
+
+def sample_vibranium(diffractometer):
+    a0 = TWO_PI
+    cubic = new_lattice(a0)
+    return new_sample(diffractometer, "vibranium", lattice=cubic)

hkl/user.py

@@ -11,6 +11,7 @@
     ~cahkl
     ~cahkl_table
     ~calc_UB
+    ~current_diffractometer
     ~list_samples
     ~new_sample
     ~or_swap
@@ -29,6 +30,7 @@
     cahkl_table
     calc_UB
     change_sample
+    current_diffractometer
     list_samples
     new_sample
     or_swap
@@ -124,6 +126,11 @@ def change_sample(sample):
     show_sample(sample)
 
 
+def current_diffractometer():
+    """Return the currently-selected diffractometer (or ``None``)."""
+    return _geom_
+
+
 def list_samples(verbose=True):
     """List all defined crystal samples."""
     _check_geom_selected()
@@ -256,9 +263,10 @@ def show_sample(sample_name=None, verbose=True):
 
 def show_selected_diffractometer(instrument=None):
     """Print the name of the selected diffractometer."""
-    if _geom_ is None:
+    geom = current_diffractometer()
+    if geom is None:
         print("No diffractometer selected.")
-    print(_geom_.name)
+    print(geom.name)
 
 
 def update_sample(a, b, c, alpha, beta, gamma):
@@ -278,10 +286,10 @@ def update_sample(a, b, c, alpha, beta, gamma):
 def pa():
     """Report (all) the diffractometer settings."""
     _check_geom_selected()
-    _geom_.pa()
+    current_diffractometer().pa()
 
 
 def wh():
     """Report (brief) where is the diffractometer."""
     _check_geom_selected()
-    _geom_.wh()
+    current_diffractometer().wh()