From 3a1ea20ae4a8eccfc17990b1e6c59fa66cca039d Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 08:14:46 -0700 Subject: [PATCH 1/6] MAINT: removed use of deprecated method from_csv --- q2_types/sample_data/tests/test_transformer.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index 4aa5b290..363fdc3f 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -26,7 +26,8 @@ def test_pd_series_to_alpha_diversity_format(self): name='shannon', index=exp_index) obs = transformer(exp) - obs = pd.Series.from_csv(str(obs), sep='\t', header=0) + obs = pd.read_csv(str(obs), sep='\t', parse_dates=True, header=0, + index_col=0, squeeze=True) assert_series_equal(exp, obs) From e9fb257fddd5906d8fbdb9385aff789ff35aa8ca Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 08:57:44 -0700 Subject: [PATCH 2/6] SQUASH: used linter for changes in PR --- q2_types/sample_data/tests/test_transformer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index 363fdc3f..a5e05ecc 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -26,7 +26,7 @@ def test_pd_series_to_alpha_diversity_format(self): name='shannon', index=exp_index) obs = transformer(exp) - obs = pd.read_csv(str(obs), sep='\t', parse_dates=True, header=0, + obs = pd.read_csv(str(obs), sep='\t', parse_dates=True, header=0, index_col=0, squeeze=True) assert_series_equal(exp, obs) From f2dc9b7de0a06fb250b3c365eb6b9a986abea3e6 Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 09:35:03 -0700 Subject: [PATCH 3/6] SQUASH: removed unnecessary keyword arguments --- q2_types/sample_data/tests/test_transformer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index a5e05ecc..faeee960 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -26,8 +26,8 @@ def test_pd_series_to_alpha_diversity_format(self): name='shannon', index=exp_index) obs = transformer(exp) - obs = pd.read_csv(str(obs), sep='\t', parse_dates=True, header=0, - index_col=0, squeeze=True) + obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0, + squeeze=True) assert_series_equal(exp, obs) From 5a69ca7fc5908191fc7f1d3c171184b1d20bfff5 Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 11:59:07 -0700 Subject: [PATCH 4/6] SQUASH: added comment to describe squeeze kwarg --- q2_types/sample_data/tests/test_transformer.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index faeee960..5dd18bd2 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -26,6 +26,10 @@ def test_pd_series_to_alpha_diversity_format(self): name='shannon', index=exp_index) obs = transformer(exp) + ''' + Squeeze equals true in function call below to convert single column + dataframe to series + ''' obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0, squeeze=True) From ce717c44575dc87bd485cc0961d807b6ebcf217a Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 12:39:23 -0700 Subject: [PATCH 5/6] SQUASH: changed comment and comment format --- q2_types/sample_data/tests/test_transformer.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index 5dd18bd2..359fb44d 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -26,10 +26,9 @@ def test_pd_series_to_alpha_diversity_format(self): name='shannon', index=exp_index) obs = transformer(exp) - ''' - Squeeze equals true in function call below to convert single column - dataframe to series - ''' + + # Squeeze equals true in function call below to return series instead + # of dataframe obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0, squeeze=True) From acc4783430db88255f5b2ea5f3a510ff68546644 Mon Sep 17 00:00:00 2001 From: David Rodriguez Date: Fri, 6 Sep 2019 13:00:03 -0700 Subject: [PATCH 6/6] SQUASH: edit comment --- q2_types/sample_data/tests/test_transformer.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/q2_types/sample_data/tests/test_transformer.py b/q2_types/sample_data/tests/test_transformer.py index 359fb44d..1d032ff9 100644 --- a/q2_types/sample_data/tests/test_transformer.py +++ b/q2_types/sample_data/tests/test_transformer.py @@ -27,8 +27,7 @@ def test_pd_series_to_alpha_diversity_format(self): obs = transformer(exp) - # Squeeze equals true in function call below to return series instead - # of dataframe + # Squeeze equals true to return series instead of dataframe obs = pd.read_csv(str(obs), sep='\t', header=0, index_col=0, squeeze=True)