Support Python 3.9

.github/workflows/CI_build.yml

@@ -24,6 +24,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e .[dev]
+      - name: Show pip list
+        run: |
+          pip list
       - name: Test with coverage
         run: |
           pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
@@ -50,7 +53,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7', '3.8']
+        python-version: ['3.7', '3.8', '3.9']
         exclude:
           # already tested in first_check job
           - python-version: 3.8
@@ -160,7 +163,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7', '3.8']
+        python-version: ['3.7', '3.8', '3.9']
     runs-on: ${{ matrix.os }}
     needs: anaconda_build
     steps:

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## Added
+
+- Now supports Python 3.9 (including CI test runs) [#40](https://github.com/iomega/spec2vec/issues/40)
+
 ## [0.5.0] - 2021-06-18
 
 ## Changed

README.rst

@@ -115,7 +115,7 @@ Installation
 
 Prerequisites:  
 
-- Python 3.7 or 3.8  
+- Python 3.7, 3.8, or 3.9  
 - Recommended: Anaconda
 
 We recommend installing spec2vec from Anaconda Cloud with

conda/environment-build.yml

@@ -5,4 +5,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - python >=3.7,<3.9
+  - python >=3.7

conda/environment-dev.yml

@@ -10,7 +10,7 @@ dependencies:
   - numba >=0.51
   - numpy
   - pip
-  - python >=3.7,<3.9
+  - python >=3.7
   - tqdm
   - pip:
     - -e ..[dev]

conda/environment.yml

@@ -8,5 +8,5 @@ dependencies:
   - matchms >=0.6.2
   - numba >=0.51
   - numpy
-  - python >=3.7,<3.9
+  - python >=3.7
   - tqdm

conda/meta.yaml

@@ -31,7 +31,7 @@ requirements:
     - numpy {{ numpy }}
     - setuptools
   host:
-    - python >=3.7,<3.9
+    - python >=3.7
     - pip
     - pytest-runner
     - setuptools
@@ -41,7 +41,7 @@ requirements:
     - numba >=0.51
     - numpy
     - pip
-    - python >=3.7,<3.9
+    - python >=3.7
     - tqdm
 
 test:

setup.py

@@ -55,6 +55,7 @@
     ],
     extras_require={"dev": ["bump2version",
                             "isort>=4.2.5,<5",
+                            "pylint<2.12.0",
                             "prospector[with_pyroma]",
                             "pytest",
                             "pytest-cov",

spec2vec/SpectrumDocument.py

@@ -57,10 +57,9 @@ def __init__(self, spectrum, n_decimals: int = 2):
 
     def _make_words(self):
         """Create word from peaks (and losses)."""
-        format_string = "{}@{:." + "{}".format(self.n_decimals) + "f}"
-        peak_words = [format_string.format("peak", mz) for mz in self._obj.peaks.mz]
+        peak_words = [f"peak@{mz:.{self.n_decimals}f}" for mz in self._obj.peaks.mz]
         if self._obj.losses is not None:
-            loss_words = [format_string.format("loss", mz) for mz in self._obj.losses.mz]
+            loss_words = [f"loss@{mz:.{self.n_decimals}f}" for mz in self._obj.losses.mz]
         else:
             loss_words = []
         self.words = peak_words + loss_words

spec2vec/model_building.py

@@ -116,12 +116,11 @@ def set_spec2vec_defaults(**settings):
     assert "alpha" not in settings, "Expect 'learning_rate_initial' instead of 'alpha'."
 
     # Set default parameters or replace by **settings input
-    for key in defaults:
+    for key, value in defaults.items():
         if key in settings:
-            print("The value of {} is set from {} (default) to {}".format(key, defaults[key],
-                                                                          settings[key]))
+            print(f"The value of {key} is set from {value} (default) to {settings[key]}")
         else:
-            settings[key] = defaults[key]
+            settings[key] = value
     return settings
 
 
@@ -166,7 +165,7 @@ def set_learning_rate_decay(learning_rate_initial: float, learning_rate_decay: f
     min_alpha = learning_rate_initial - num_of_epochs * learning_rate_decay
     if min_alpha < 0:
         print("Warning! Number of total iterations is too high for given learning_rate decay.")
-        print("Learning_rate_decay will be set from {} to {}.".format(learning_rate_decay,
-                                                                      learning_rate_initial/num_of_epochs))
+        print("Learning_rate_decay will be set from {learning_rate_decay} ",
+              "to {learning_rate_initial/num_of_epochs}.")
         min_alpha = 0
     return learning_rate_initial, min_alpha

spec2vec/utils.py

@@ -24,7 +24,7 @@ def on_epoch_end(self, model):
         print('\r',
               ' Epoch ' + str(self.epoch+1) + ' of ' + str(self.num_of_epochs) + '.',
               end="")
-        print('Change in loss after epoch {}: {}'.format(self.epoch+1, loss - self.loss))
+        print(f'Change in loss after epoch {self.epoch + 1}: {loss - self.loss}')
         self.epoch += 1
         self.loss = loss
 
@@ -56,7 +56,7 @@ def on_epoch_end(self, model):
 
         if self.filename and self.epoch in self.iterations:
             if self.epoch < self.num_of_epochs:
-                filename = self.filename.split(".model")[0] + "_iter_{}.model".format(self.epoch)
+                filename = f"{self.filename.split('.model')[0]}_iter_{self.epoch}.model"
             else:
                 filename = self.filename
             print("Saving model with name:", filename)

spec2vec/vector_operations.py

@@ -41,8 +41,8 @@ def _check_model_coverage():
             weights_missing_raised = numpy.power(weights_missing, intensity_weighting_power)
             missing_percentage = 100 * weights_missing_raised.sum() / (weights_raised.sum()
                                                                        + weights_missing_raised.sum())
-            print("Found {} word(s) missing in the model.".format(len(idx_not_in_model)),
-                  "Weighted missing percentage not covered by the given model is {:.2f}%.".format(missing_percentage))
+            print(f"Found {len(idx_not_in_model)} word(s) missing in the model.",
+                  f"Weighted missing percentage not covered by the given model is {missing_percentage:.2f}%.")
 
             message = ("Missing percentage is larger than set maximum.",
                        "Consider retraining the used model or increasing the allowed percentage.")

tests/test_version_string_consistency.py

@@ -9,7 +9,7 @@ def test_version_string_consistency():
     repository_root = os.path.join(os.path.dirname(__file__), "..")
     fixture = os.path.join(repository_root, "conda", "meta.yaml")
 
-    with open(fixture, "r") as f:
+    with open(fixture, "r", encoding="utf-8") as f:
         metayaml_contents = f.read()
 
     match = re.search(r"^{% set version = \"(?P<semver>.*)\" %}$", metayaml_contents, re.MULTILINE)