diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml index 0a6c083a..87952292 100644 --- a/.github/workflows/e2e_testing.yml +++ b/.github/workflows/e2e_testing.yml @@ -24,6 +24,7 @@ jobs: NUMBA_BOUNDSCHECK: 1 NUMBA_DEVELOPER_MODE: 1 NUMBA_FULL_TRACEBACKS: 1 + TQDM_MININTERVAL: 10 # avoid lots of tqdm outputs steps: - uses: actions/checkout@v4 - name: Conda info diff --git a/alphadia/fdrexperimental.py b/alphadia/fdrexperimental.py index 901258eb..c8d4cc20 100644 --- a/alphadia/fdrexperimental.py +++ b/alphadia/fdrexperimental.py @@ -368,7 +368,7 @@ def fit(self, x: np.ndarray, y: np.ndarray): y_test = torch.from_numpy(y_test).float().to(self.device) batch_count = 0 - for epoch in tqdm(range(self.epochs), mininterval=5): + for epoch in tqdm(range(self.epochs)): train_loss_sum = 0.0 test_loss_sum = 0.0 @@ -1122,7 +1122,7 @@ def fit(self, x: np.ndarray, y: np.ndarray): batch_count = 0 - for epoch in tqdm(range(self.epochs), mininterval=5): + for epoch in tqdm(range(self.epochs)): # shuffle batches order = np.random.permutation(num_batches) batch_start_list = batch_start_list[order] diff --git a/alphadia/outputaccumulator.py b/alphadia/outputaccumulator.py index 63010c63..4d0ef135 100644 --- a/alphadia/outputaccumulator.py +++ b/alphadia/outputaccumulator.py @@ -553,8 +553,7 @@ def ms2_quality_control( precursor_df["frag_stop_idx"], strict=True, ) - ), - mininterval=5, + ) ): # get XIC correlations and intensities for the precursor fragment_correlation_view = fragment_correlation_df.iloc[start_idx:stop_idx] diff --git a/alphadia/transferlearning/train.py b/alphadia/transferlearning/train.py index 343be3a2..69eaeed7 100644 --- a/alphadia/transferlearning/train.py +++ b/alphadia/transferlearning/train.py @@ -287,7 +287,7 @@ def _order_intensities( The reordered fragment intensity dataframe. """ reordered = unordered_frag_df.copy() - for i in tqdm(range(len(reordered_precursor_df)), mininterval=5): + for i in tqdm(range(len(reordered_precursor_df))): new_start_idx = reordered_precursor_df.iloc[i]["frag_start_idx"] new_end_idx = reordered_precursor_df.iloc[i]["frag_stop_idx"]