FIX: make sure values are of correct type before json.dumping (#26)

* FIX: make sure values are of correct type before json.dumping * update copyright year * CI updates
bokulich-lab · Jul 12, 2022 · 3cd8ebf · 3cd8ebf
1 parent d9dfa9d
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -18,13 +18,9 @@ jobs:
         with:
           python-version: 3.8
       - name: install dependencies
-        run: python -m pip install --upgrade pip
+        run: pip install -q flake8 https://github.com/qiime2/q2lint/archive/master.zip
       - name: lint
-        run: |
-          pip install -q https://github.com/qiime2/q2lint/archive/master.zip
-          q2lint
-          pip install -q flake8
-          flake8
+        run: make lint
 
   rust-test:
     runs-on: ubuntu-latest
@@ -47,11 +43,19 @@ jobs:
         with:
           # necessary for versioneer
           fetch-depth: 0
+
+      - name: Hack - template coverage output path
+        run: echo "COV=coverage xml -o $GITHUB_WORKSPACE/coverage.xml" >> $GITHUB_ENV
+
       # TODO: update this to @v1 when it lands
       - uses: qiime2/action-library-packaging@alpha1
         with:
           package-name: q2-protein-pca
-          additional-tests: pytest --pyargs q2_protein_pca
-          # TODO: update this to `released` when tagging release
-          build-target: staged
+          additional-tests: ${{ env.COV }}
+          build-target: dev
           library-token: ${{ secrets.LIBRARY_TOKEN }}
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          fail_ci_if_error: true
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, QIIME 2 development team.
+Copyright (c) 2022, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/ci/recipe/conda_build_config.yaml b/ci/recipe/conda_build_config.yaml
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -1,6 +1,5 @@
 {% set data = load_setup_py_data() %}
 {% set version = data.get('version') or 'placehold' %}
-{% set release = '.'.join(version.split('.')[:2]) %}
 
 package:
   name: q2-protein-pca
@@ -14,7 +13,7 @@ build:
 
 requirements:
   build:
-    - maturin
+    - maturin ==0.10.3
     - rust ==1.51.0
 
   host:
@@ -27,16 +26,21 @@ requirements:
     - pandas
     - numpy
     - matplotlib
-    - qiime2 {{ release }}.*
-    - q2templates {{ release }}.*
-    - q2-types {{ release }}.*
-    - q2-alignment {{ release }}.*
+    - qiime2 {{ qiime2_epoch }}.*
+    - q2templates {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
+    - q2-alignment {{ qiime2_epoch }}.*
 
 test:
+  requires:
+    - coverage
+    - pytest-cov
   imports:
     - q2_protein_pca
     - qiime2.plugins.protein_pca
     - aln_ranking
+  commands:
+    - pytest --cov q2_protein_pca --pyargs q2_protein_pca
 
 about:
   home: https://github.com/bokulich-lab/q2-protein-pca

diff --git a/q2_protein_pca/__init__.py b/q2_protein_pca/__init__.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_alignment.py b/q2_protein_pca/_alignment.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_format.py b/q2_protein_pca/_format.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_pca.py b/q2_protein_pca/_pca.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_plot.py b/q2_protein_pca/_plot.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
@@ -27,14 +27,17 @@ def _generate_spec(plot_values: pd.DataFrame,
                    x_col_name: str,
                    y_col_name: str,
                    sequence_ids: list) -> dict:
+    # replace NaNs
+    plot_values = plot_values.replace({np.nan: None})
+    # convert types to object (json.dumps cannot dump pandas' Int64)
+    plot_values.iloc[:, 5:] = plot_values.iloc[:, 5:].astype(object)
     spec = {
         '$schema': 'https://vega.github.io/schema/vega/v4.2.json',
         'width': 300,
         'height': 300,
         'data': [
             {'name': 'values',
-             'values': plot_values.replace(
-                 {np.nan: None}).to_dict(orient='records')},
+             'values': plot_values.to_dict(orient='records')},
         ],
         'scales': [
             {'name': 'xScale',

diff --git a/q2_protein_pca/_ranking.py b/q2_protein_pca/_ranking.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_transformer.py b/q2_protein_pca/_transformer.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/_type.py b/q2_protein_pca/_type.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/plugin_setup.py b/q2_protein_pca/plugin_setup.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/tests/__init__.py b/q2_protein_pca/tests/__init__.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/tests/data/expected_spec.py b/q2_protein_pca/tests/data/expected_spec.py
@@ -1,26 +1,46 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+from copy import deepcopy
 
 EXPECTED_SPEC = {
     '$schema': 'https://vega.github.io/schema/vega/v4.2.json',
     'width': 300,
     'height': 300,
     'data': [
-        {'name': 'values',
-         'values': [{'PC1': 0.0, 'PC2': 0.0}, {'PC1': 0.1, 'PC2': 0.2}, {'PC1': -0.5, 'PC2': -0.1}]},
+        {
+            'name': 'values',
+            'values': [
+                {
+                    'id': 'pos1', 'PC1': 0, 'PC2': 0,
+                    'euclid_dist': 0, 'max_dist': 0.26, 'COL3': 1
+                },
+                {
+                    'id': 'pos2', 'PC1': 0.1, 'PC2': 0.2,
+                    'euclid_dist': 0.05, 'max_dist': 0.26, 'COL3': 2
+                },
+                {
+                    'id': 'pos3', 'PC1': -0.5, 'PC2': -0.1,
+                    'euclid_dist': 0.26, 'max_dist': 0.26, 'COL3': 3
+                }
+            ]
+        },
     ],
     'scales': [
-        {'name': 'xScale',
-         'domain': {'data': 'values', 'field': 'PC1'},
-         'range': 'width'},
-        {'name': 'yScale',
-         'domain': {'data': 'values', 'field': 'PC2'},
-         'range': 'height'}],
+        {
+            'name': 'xScale',
+            'domain': {'data': 'values', 'field': 'PC1'},
+            'range': 'width'
+        },
+        {
+            'name': 'yScale',
+            'domain': {'data': 'values', 'field': 'PC2'},
+            'range': 'height'
+        }],
     'axes': [
         {'scale': 'xScale', 'orient': 'bottom', 'title': 'PC1'},
         {'scale': 'yScale', 'orient': 'left', 'title': 'PC2'}],
@@ -30,58 +50,81 @@
             "description": "Conservation level [%]",
             "value": 90,
             "bind": {
-                    "input": "range",
-                    "min": 0,
-                    "max": 100,
-                    "step": 1,
-                    "debounce": 10,
-                    "element": "#conservation-level-slider"
+                "input": "range",
+                "min": 0,
+                "max": 100,
+                "step": 1,
+                "debounce": 10,
+                "element": "#conservation-level-slider"
             }
         },
         {
             "name": "sequenceID",
             "description": "Sequence ID",
             "bind": {
-                    "input": "select",
-                    "options": ["id1", "id2", "id3"],
-                    "element": "#sequence-id-selector"
+                "input": "select",
+                "options": ["id1", "id2", "id3"],
+                "element": "#sequence-id-selector"
             }
         },
         {
             "name": "hideMissingPositions",
             "description": "Hide missing positions",
             "bind": {
-                    "input": "checkbox",
-                    "element": "#hide-positions-selector"
+                "input": "checkbox",
+                "element": "#hide-positions-selector"
             },
         }
     ],
     'marks': [
-        {'type': 'symbol',
-         'from': {'data': 'values'},
-         'encode': {
-                 'hover': {
-                     'fill': {'value': '#d62728'},
-                     'opacity': {'value': 0.8}},
-                 'enter': {
-                     'x': {'scale': 'xScale', 'field': 'PC1'},
-                     'y': {'scale': 'yScale', 'field': 'PC2'}},
-                 'update': {
-                     'fill': [
-                         {
-                             'test': "datum.euclid_dist / datum.max_distance <= (1 - conservationLevel / 100)",
-                             'value': '#3182bd'
-                         },
-                         {'value': 'black'}
-                     ],
-                     'opacity': [
-                         {
-                             'test': "datum[sequenceID] == null && hideMissingPositions",
-                             'value': 0.0
-                         },
-                         {'value': 0.8}],
-                     'tooltip': {
-                         'signal': f"{{'title': 'position ' + datum['id'], "
-                                   f"'PC1': datum['PC1'], "
-                                   f"'PC2': datum['PC2']}}"}
-                 }}}]}
+        {
+            'type': 'symbol',
+            'from': {'data': 'values'},
+            'encode': {
+                'hover': {
+                    'fill': {'value': '#d62728'},
+                    'opacity': {'value': 0.8}
+                },
+                'enter': {
+                    'x': {'scale': 'xScale', 'field': 'PC1'},
+                    'y': {'scale': 'yScale', 'field': 'PC2'}
+                },
+                'update': {
+                    'fill': [
+                        {
+                            'test': "datum.euclid_dist / datum.max_distance <= (1 - conservationLevel / 100)",
+                            'value': '#3182bd'
+                        },
+                        {'value': 'black'}
+                    ],
+                    'opacity': [
+                        {
+                            'test': "datum[sequenceID] == null && hideMissingPositions",
+                            'value': 0.0
+                        },
+                        {'value': 0.8}],
+                    'tooltip': {
+                        'signal': f"{{'title': 'position ' + datum['id'], "
+                                  f"'PC1': datum['PC1'], "
+                                  f"'PC2': datum['PC2']}}"
+                    }
+                }
+            }
+        }]
+}
+
+EXPECTED_SPEC_WITH_NANS = deepcopy(EXPECTED_SPEC)
+EXPECTED_SPEC_WITH_NANS['data'][0]['values'] = [
+    {
+        'id': 'pos1', 'PC1': 0, 'PC2': 0,
+        'euclid_dist': 0, 'max_dist': 0.26, 'COL3': None
+    },
+    {
+        'id': 'pos2', 'PC1': 0.1, 'PC2': 0.2,
+        'euclid_dist': 0.05, 'max_dist': 0.26, 'COL3': 2
+    },
+    {
+        'id': 'pos3', 'PC1': -0.5, 'PC2': -0.1,
+        'euclid_dist': 0.26, 'max_dist': 0.26, 'COL3': 3
+    }
+]
diff --git a/q2_protein_pca/tests/test_alignment.py b/q2_protein_pca/tests/test_alignment.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

diff --git a/q2_protein_pca/tests/test_pca.py b/q2_protein_pca/tests/test_pca.py
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2021, QIIME 2 development team.
+# Copyright (c) 2022, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #