Update to new adapter API.

tanaylab · Jun 11, 2024 · 014979d · 014979d
1 parent fdff258
commit 014979d
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Showing 9 changed files with 188 additions and 82 deletions.
diff --git a/daf/adapters.py b/daf/adapters.py
@@ -18,13 +18,13 @@
 from typing import Optional
 
 from .copies import EmptyData
-from .data import DafReadOnly
+from .copies import copy_all
 from .data import DafWriter
 from .formats import MemoryDaf
-from .julia_import import _jl_pairs
-from .julia_import import jl
+from .formats import chain_writer
 from .views import ViewAxes
 from .views import ViewData
+from .views import viewer
 
 __all__ = [
     "adapter",
@@ -33,30 +33,27 @@
 
 @contextmanager
 def adapter(
-    view: DafWriter | DafReadOnly,
-    name: Optional[str] = None,
+    dset: DafWriter,
+    *,
+    input_axes: Optional[ViewAxes] = None,
+    input_data: Optional[ViewData] = None,
     capture: Callable[..., DafWriter] = MemoryDaf,
-    axes: Optional[ViewAxes] = None,
-    data: Optional[ViewData] = None,
+    output_axes: Optional[ViewAxes] = None,
+    output_data: Optional[ViewData] = None,
     empty: Optional[EmptyData] = None,
     relayout: bool = True,
     overwrite: bool = False,
 ) -> Iterator[DafWriter]:
     """
-    Invoke a computation on a ``view`` data set; copy a ``viewer`` of the updated data set into the base ``Daf`` data
-    set of the view. See the Julia
+    Invoke a computation on a view of some ``dset`` and return the result; copy a view of the results into the
+    base ``dset``. See the Julia
     `documentation <https://tanaylab.github.io/Daf.jl/v0.1.0/adapters.html#Daf.Adapters.adapter>`__ for details.
     """
-    writer = capture(name=jl.Daf.Adapters.get_adapter_capture_name(view, name=name))
-    adapted = jl.Daf.Adapters.get_adapter_input(view, name=name, writer=writer)
-    yield DafWriter(adapted)
-    jl.Daf.Adapters.copy_adapter_output(
-        view,
-        adapted,
-        name=name,
-        axes=axes,
-        data=jl._pairify_data(_jl_pairs(data)),
-        empty=empty,
-        relayout=relayout,
-        overwrite=overwrite,
-    )
+    base_name = dset.name
+    input_dset = viewer(dset, axes=input_axes, data=input_data, name=f"{base_name}.input")
+    captured_dset = capture(name=f"{base_name}.capture")
+    adapted_dset = chain_writer([input_dset, captured_dset], name=f"{base_name}.adapted")
+    result = yield adapted_dset
+    output_dset = viewer(adapted_dset, axes=output_axes, data=output_data, name=f"{base_name}.output")
+    copy_all(source=output_dset, destination=dset, empty=empty, relayout=relayout, overwrite=overwrite)
+    return result
diff --git a/daf/julia_import.py b/daf/julia_import.py
@@ -80,7 +80,7 @@
 jl_version = (jl.VERSION.major, jl.VERSION.minor, jl.VERSION.patch)
 
 jl.seval("using Pkg")
-jl.seval("Pkg.update()")
+# jl.seval("Pkg.update()")
 
 jl.seval("using Daf")
 

diff --git a/docs/v0.1.0/html/_modules/daf/adapters.html b/docs/v0.1.0/html/_modules/daf/adapters.html
@@ -97,13 +97,13 @@ <h1>Source code for daf.adapters</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span>
 
 <span class="kn">from</span> <span class="nn">.copies</span> <span class="kn">import</span> <span class="n">EmptyData</span>
-<span class="kn">from</span> <span class="nn">.data</span> <span class="kn">import</span> <span class="n">DafReadOnly</span>
+<span class="kn">from</span> <span class="nn">.copies</span> <span class="kn">import</span> <span class="n">copy_all</span>
 <span class="kn">from</span> <span class="nn">.data</span> <span class="kn">import</span> <span class="n">DafWriter</span>
 <span class="kn">from</span> <span class="nn">.formats</span> <span class="kn">import</span> <span class="n">MemoryDaf</span>
-<span class="kn">from</span> <span class="nn">.julia_import</span> <span class="kn">import</span> <span class="n">_jl_pairs</span>
-<span class="kn">from</span> <span class="nn">.julia_import</span> <span class="kn">import</span> <span class="n">jl</span>
+<span class="kn">from</span> <span class="nn">.formats</span> <span class="kn">import</span> <span class="n">chain_writer</span>
 <span class="kn">from</span> <span class="nn">.views</span> <span class="kn">import</span> <span class="n">ViewAxes</span>
 <span class="kn">from</span> <span class="nn">.views</span> <span class="kn">import</span> <span class="n">ViewData</span>
+<span class="kn">from</span> <span class="nn">.views</span> <span class="kn">import</span> <span class="n">viewer</span>
 
 <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span>
     <span class="s2">&quot;adapter&quot;</span><span class="p">,</span>
@@ -114,33 +114,30 @@ <h1>Source code for daf.adapters</h1><div class="highlight"><pre>
 <a class="viewcode-back" href="../../adapters.html#daf.adapters.adapter">[docs]</a>
 <span class="nd">@contextmanager</span>
 <span class="k">def</span> <span class="nf">adapter</span><span class="p">(</span>
-    <span class="n">view</span><span class="p">:</span> <span class="n">DafWriter</span> <span class="o">|</span> <span class="n">DafReadOnly</span><span class="p">,</span>
-    <span class="n">name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">dset</span><span class="p">:</span> <span class="n">DafWriter</span><span class="p">,</span>
+    <span class="o">*</span><span class="p">,</span>
+    <span class="n">input_axes</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewAxes</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">input_data</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewData</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">capture</span><span class="p">:</span> <span class="n">Callable</span><span class="p">[</span><span class="o">...</span><span class="p">,</span> <span class="n">DafWriter</span><span class="p">]</span> <span class="o">=</span> <span class="n">MemoryDaf</span><span class="p">,</span>
-    <span class="n">axes</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewAxes</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-    <span class="n">data</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewData</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">output_axes</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewAxes</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">output_data</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ViewData</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">empty</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">EmptyData</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">relayout</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
     <span class="n">overwrite</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Iterator</span><span class="p">[</span><span class="n">DafWriter</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Invoke a computation on a ``view`` data set; copy a ``viewer`` of the updated data set into the base ``Daf`` data</span>
-<span class="sd">    set of the view. See the Julia</span>
+<span class="sd">    Invoke a computation on a view of some ``dset`` and return the result; copy a view of the results into the</span>
+<span class="sd">    base ``dset``. See the Julia</span>
 <span class="sd">    `documentation &lt;https://tanaylab.github.io/Daf.jl/v0.1.0/adapters.html#Daf.Adapters.adapter&gt;`__ for details.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">writer</span> <span class="o">=</span> <span class="n">capture</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">jl</span><span class="o">.</span><span class="n">Daf</span><span class="o">.</span><span class="n">Adapters</span><span class="o">.</span><span class="n">get_adapter_capture_name</span><span class="p">(</span><span class="n">view</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">))</span>
-    <span class="n">adapted</span> <span class="o">=</span> <span class="n">jl</span><span class="o">.</span><span class="n">Daf</span><span class="o">.</span><span class="n">Adapters</span><span class="o">.</span><span class="n">get_adapter_input</span><span class="p">(</span><span class="n">view</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="n">writer</span><span class="o">=</span><span class="n">writer</span><span class="p">)</span>
-    <span class="k">yield</span> <span class="n">DafWriter</span><span class="p">(</span><span class="n">adapted</span><span class="p">)</span>
-    <span class="n">jl</span><span class="o">.</span><span class="n">Daf</span><span class="o">.</span><span class="n">Adapters</span><span class="o">.</span><span class="n">copy_adapter_output</span><span class="p">(</span>
-        <span class="n">view</span><span class="p">,</span>
-        <span class="n">adapted</span><span class="p">,</span>
-        <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span>
-        <span class="n">axes</span><span class="o">=</span><span class="n">axes</span><span class="p">,</span>
-        <span class="n">data</span><span class="o">=</span><span class="n">jl</span><span class="o">.</span><span class="n">_pairify_data</span><span class="p">(</span><span class="n">_jl_pairs</span><span class="p">(</span><span class="n">data</span><span class="p">)),</span>
-        <span class="n">empty</span><span class="o">=</span><span class="n">empty</span><span class="p">,</span>
-        <span class="n">relayout</span><span class="o">=</span><span class="n">relayout</span><span class="p">,</span>
-        <span class="n">overwrite</span><span class="o">=</span><span class="n">overwrite</span><span class="p">,</span>
-    <span class="p">)</span></div>
+    <span class="n">base_name</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">input_dset</span> <span class="o">=</span> <span class="n">viewer</span><span class="p">(</span><span class="n">dset</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">input_axes</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">input_data</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.input&quot;</span><span class="p">)</span>
+    <span class="n">captured_dset</span> <span class="o">=</span> <span class="n">capture</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.capture&quot;</span><span class="p">)</span>
+    <span class="n">adapted_dset</span> <span class="o">=</span> <span class="n">chain_writer</span><span class="p">([</span><span class="n">input_dset</span><span class="p">,</span> <span class="n">captured_dset</span><span class="p">],</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.adapted&quot;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="k">yield</span> <span class="n">adapted_dset</span>
+    <span class="n">output_dset</span> <span class="o">=</span> <span class="n">viewer</span><span class="p">(</span><span class="n">adapted_dset</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">output_axes</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">output_data</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.output&quot;</span><span class="p">)</span>
+    <span class="n">copy_all</span><span class="p">(</span><span class="n">source</span><span class="o">=</span><span class="n">output_dset</span><span class="p">,</span> <span class="n">destination</span><span class="o">=</span><span class="n">dset</span><span class="p">,</span> <span class="n">empty</span><span class="o">=</span><span class="n">empty</span><span class="p">,</span> <span class="n">relayout</span><span class="o">=</span><span class="n">relayout</span><span class="p">,</span> <span class="n">overwrite</span><span class="o">=</span><span class="n">overwrite</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">result</span></div>
 
 </pre></div>
 

diff --git a/docs/v0.1.0/html/_modules/daf/julia_import.html b/docs/v0.1.0/html/_modules/daf/julia_import.html
@@ -159,7 +159,7 @@ <h1>Source code for daf.julia_import</h1><div class="highlight"><pre>
 <span class="n">jl_version</span> <span class="o">=</span> <span class="p">(</span><span class="n">jl</span><span class="o">.</span><span class="n">VERSION</span><span class="o">.</span><span class="n">major</span><span class="p">,</span> <span class="n">jl</span><span class="o">.</span><span class="n">VERSION</span><span class="o">.</span><span class="n">minor</span><span class="p">,</span> <span class="n">jl</span><span class="o">.</span><span class="n">VERSION</span><span class="o">.</span><span class="n">patch</span><span class="p">)</span>
 
 <span class="n">jl</span><span class="o">.</span><span class="n">seval</span><span class="p">(</span><span class="s2">&quot;using Pkg&quot;</span><span class="p">)</span>
-<span class="n">jl</span><span class="o">.</span><span class="n">seval</span><span class="p">(</span><span class="s2">&quot;Pkg.update()&quot;</span><span class="p">)</span>
+<span class="c1"># jl.seval(&quot;Pkg.update()&quot;)</span>
 
 <span class="n">jl</span><span class="o">.</span><span class="n">seval</span><span class="p">(</span><span class="s2">&quot;using Daf&quot;</span><span class="p">)</span>
 

diff --git a/docs/v0.1.0/html/adapters.html b/docs/v0.1.0/html/adapters.html
@@ -304,20 +304,88 @@ <h1>adapters
 <span class="sig-paren">(
 </span>
 <em class="sig-param">
-<span class="pre">view:
+<span class="pre">dset:
 </span> 
-<span class="pre">~daf.data.DafWriter
+<span class="pre">~daf.data.DafWriter,
+</span> 
+<span class="pre">*,
+</span> 
+<span class="pre">input_axes:
+</span> 
+<span class="pre">~typing.Mapping[str,
+</span> 
+<span class="pre">str
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.queries.Axis
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.queries.Lookup
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.queries.Names
 </span> 
 <span class="pre">|
 </span> 
-<span class="pre">~daf.data.DafReadOnly,
+<span class="pre">~daf.operations.QuerySequence
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">None]
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">None
 </span> 
-<span class="pre">name:
+<span class="pre">=
+</span> 
+<span class="pre">None,
+</span> 
+<span class="pre">input_data:
+</span> 
+<span class="pre">~typing.Mapping[str
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~typing.Tuple[str,
+</span> 
+<span class="pre">str]
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~typing.Tuple[str,
+</span> 
+<span class="pre">str,
+</span> 
+<span class="pre">str],
 </span> 
 <span class="pre">str
 </span> 
 <span class="pre">|
 </span> 
+<span class="pre">~daf.queries.Axis
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.queries.Lookup
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.queries.Names
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">~daf.operations.QuerySequence
+</span> 
+<span class="pre">|
+</span> 
+<span class="pre">None]
+</span> 
+<span class="pre">|
+</span> 
 <span class="pre">None
 </span> 
 <span class="pre">=
@@ -336,7 +404,7 @@ <h1>adapters
 </span> 
 <span class="pre">'daf.formats.MemoryDaf'&gt;,
 </span> 
-<span class="pre">axes:
+<span class="pre">output_axes:
 </span> 
 <span class="pre">~typing.Mapping[str,
 </span> 
@@ -370,7 +438,7 @@ <h1>adapters
 </span> 
 <span class="pre">None,
 </span> 
-<span class="pre">data:
+<span class="pre">output_data:
 </span> 
 <span class="pre">~typing.Mapping[str
 </span> 
@@ -548,20 +616,16 @@ <h1>adapters
 </dt>
 
 <dd>
-<p>Invoke a computation on a 
+<p>Invoke a computation on a view of some 
 <code class="docutils literal notranslate">
-<span class="pre">view
+<span class="pre">dset
 </span>
-</code> data set; copy a 
+</code> and return the result; copy a view of the results into the
+base 
 <code class="docutils literal notranslate">
-<span class="pre">viewer
+<span class="pre">dset
 </span>
-</code> of the updated data set into the base 
-<code class="docutils literal notranslate">
-<span class="pre">Daf
-</span>
-</code> data
-set of the view. See the Julia
+</code>. See the Julia
 
 <a class="reference external" href="https://tanaylab.github.io/Daf.jl/v0.1.0/adapters.html#Daf.Adapters.adapter">documentation
 </a> for details.

diff --git a/docs/v0.1.0/html/searchindex.js b/docs/v0.1.0/html/searchindex.js
diff --git a/tests/test_adapters.py b/tests/test_adapters.py
@@ -11,6 +11,6 @@
 def test_adapters() -> None:  # pylint: disable=too-many-statements
     dset = MemoryDaf(name="memory!")
     dset.set_scalar("INPUT", 1)
-    with adapter(viewer(dset, data={"input": ": INPUT"}), data={"OUTPUT": ": output"}) as adapted:
+    with adapter(dset, input_data={"input": ": INPUT"}, output_data={"OUTPUT": ": output"}) as adapted:
         adapted.set_scalar("output", adapted.get_scalar("input"))
     assert dset.get_scalar("OUTPUT") == 1