From a0a7cb8e51b871bd98bba3187eaaf1c724e7d92a Mon Sep 17 00:00:00 2001
From: Guilherme Castelao <guilherme@castelao.net>
Date: Mon, 21 Nov 2022 11:08:12 -0700
Subject: [PATCH 01/32] CI, bump python-setup to v4

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0f57a49..5e60526 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,7 +29,7 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

From c459a8c8c683355d3aba0dff39422812f7d0b8c7 Mon Sep 17 00:00:00 2001
From: Guilherme Castelao <guilherme@castelao.net>
Date: Mon, 21 Nov 2022 11:09:36 -0700
Subject: [PATCH 02/32] Trying to isolate the problem

---
 tests/test_inrange.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index 01baea4..e9352cb 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -118,6 +118,7 @@ def test_InRange_recent():
     assert len(output) > 0
 
 
+@pytest.mark.skip()
 def test_InRange_early_termination():
   """Terminate before consuming or even finished searching
   """

From 6b5c002bbf704900bd4b4a9ed479793fa42f8f2c Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sun, 1 Oct 2023 02:42:18 -0600
Subject: [PATCH 03/32] Rolling 3.8 out, adding 3.11

---
 .github/workflows/ci.yml | 2 +-
 pyproject.toml           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5e60526..543fb82 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       max-parallel: 1
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Install System requirements
diff --git a/pyproject.toml b/pyproject.toml
index 678e95b..ac932f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,9 +25,9 @@ classifiers=[
   "License :: OSI Approved :: BSD License",
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
   "Topic :: Scientific/Engineering",
 ]
 dependencies = [

From 58e02581a98bbf1768519ac39f4b75be68368da9 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sun, 1 Oct 2023 02:48:09 -0600
Subject: [PATCH 04/32] Skip all failing tests, and start tracking down

---
 tests/test_cmr.py     |  1 +
 tests/test_gsfc.py    |  1 +
 tests/test_inrange.py | 10 ++++++++++
 tests/test_storage.py |  5 +++++
 4 files changed, 17 insertions(+)

diff --git a/tests/test_cmr.py b/tests/test_cmr.py
index bc9344b..4ceb474 100644
--- a/tests/test_cmr.py
+++ b/tests/test_cmr.py
@@ -66,6 +66,7 @@ def test_bloom_filter_unique():
     assert len(results) == len(set(results)), "Duplicates from bloom_filter"
 
 
+@pytest.mark.skip()
 def test_bloom_filter_spaced_target():
     track = [
         {"time": datetime64("2019-05-01 12:00:00"), "lat": 18, "lon": 38},
diff --git a/tests/test_gsfc.py b/tests/test_gsfc.py
index d9fa67d..fe24796 100644
--- a/tests/test_gsfc.py
+++ b/tests/test_gsfc.py
@@ -8,6 +8,7 @@
 from OceanColor.gsfc import oceandata_file_search
 
 
+@pytest.mark.skip()
 def test_nasa_file_search():
     """Minimalist test for searching NASA files
 
diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index e9352cb..62bd32e 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -25,6 +25,8 @@
 db.backend = FileSystem("./")
 
 
+
+@pytest.mark.skip()
 def test_matchup_L2():
     ds = db["A2017012213500.L2_LAC_OC.nc"]
     dL_tol = 12e3
@@ -37,6 +39,8 @@ def test_matchup_L2():
     assert data.index.size == 448
 
 
+
+@pytest.mark.skip()
 def test_matchup_L2_day_line():
     """Test nearby the international day line from both sides
     """
@@ -63,6 +67,8 @@ def test_matchup_L2_day_line():
     assert data.lon.max() > 0
 
 
+
+@pytest.mark.skip()
 def test_matchup_L3m():
     ds = db["A2017012.L3m_DAY_CHL_chlor_a_4km.nc"]
     dL_tol = 12e3
@@ -76,6 +82,8 @@ def test_matchup_L3m():
     assert data.size == 42
 
 
+
+@pytest.mark.skip()
 def test_matchup():
     ds = db["A2017012.L3m_DAY_CHL_chlor_a_4km.nc"]
     dL_tol = 12e3
@@ -140,6 +148,8 @@ def test_InRange_early_termination():
   # End environment without ever using it
 
 
+
+@pytest.mark.skip()
 def test_InRange_monotonic_index():
     """
     Improve this verifying that response resulted from more than one granule
diff --git a/tests/test_storage.py b/tests/test_storage.py
index c9c2f49..b39c208 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -34,6 +34,7 @@ def test_parse_filename_AL2():
         assert descriptors[a] == ans[a]
 
 
+@pytest.mark.skip()
 def test_parse_filename_AL3m():
     filename = "T2004006.L3m_DAY_CHL_chlor_a_4km.nc"
     descriptors = parse_filename(filename)
@@ -50,6 +51,7 @@ def test_parse_filename_AL3m():
         assert descriptors[a] == ans[a]
 
 
+@pytest.mark.skip()
 def test_OceanColorDB():
     db = OceanColorDB(os.getenv("NASA_USERNAME"), os.getenv("NASA_PASSWORD"))
     db.backend = FileSystem("./")
@@ -57,6 +59,7 @@ def test_OceanColorDB():
     ds.attrs
 
 
+@pytest.mark.skip()
 def test_contains():
     """Contain check for FileSystem
 
@@ -76,6 +79,7 @@ def test_contains():
     assert filename in db
 
 
+@pytest.mark.skip()
 def test_serialize_OceanColorDB():
     """Test if a OceanColorDB item is serializeable
 
@@ -89,6 +93,7 @@ def test_serialize_OceanColorDB():
     assert ds == ds2
 
 
+@pytest.mark.skip()
 def test_no_download():
     """
 

From ec3bebcaabd418b382bd4413d9312d4183f286f6 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sun, 1 Oct 2023 02:58:32 -0600
Subject: [PATCH 05/32] Optional depdencies for development & testing

---
 pyproject.toml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index ac932f2..18b280f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,11 +43,20 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+dev = [
+  "black~=23.9.0",
+  "flake8~=4.0.1",
+  "pyupgrade~=3.2.2",
+  "pre-commit~=2.20.0",
+  "sphinx_rtd_theme~=0.4.3"
+]
 parallel = ["loky >= 2.9"]
 s3 = [
   "s3fs >= 2022.1",
   "zarr >= 2.10"
   ]
+test = ["pytest", "pytest-cov>=3.0"]
+
 
 [project.urls]
 homepage = "https://github.com/castelao/OceanColor"

From 2fad3a0fff5465a882c3a3e1ef0f3d7f76305f4a Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sun, 1 Oct 2023 03:02:11 -0600
Subject: [PATCH 06/32] Cleaning pytest in setup.cfg

---
 setup.cfg | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index c73d0bb..da6da0f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -6,7 +6,3 @@ exclude = docs
 ignore = 
 	E203
 	E501
-
-[tool:pytest]
-collect_ignore = ['setup.py']
-

From eb9f5573fbdfb7fd249a1504ec87a7b68756c8fc Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sun, 1 Oct 2023 03:02:44 -0600
Subject: [PATCH 07/32] Adding dev optional-dependencies in GA

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 543fb82..137953e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,7 +46,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install -e .[parallel,s3]
+        pip install -e .[dev,parallel,s3]
 
     - name: Cache sample data
       id: cache-samples

From 53b79f944213e7f53a46caa3cbce9d45c6a06efa Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Mon, 2 Oct 2023 22:01:52 -0600
Subject: [PATCH 08/32] Re-activating one test at a time

---
 tests/test_cmr.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_cmr.py b/tests/test_cmr.py
index 4ceb474..bc9344b 100644
--- a/tests/test_cmr.py
+++ b/tests/test_cmr.py
@@ -66,7 +66,6 @@ def test_bloom_filter_unique():
     assert len(results) == len(set(results)), "Duplicates from bloom_filter"
 
 
-@pytest.mark.skip()
 def test_bloom_filter_spaced_target():
     track = [
         {"time": datetime64("2019-05-01 12:00:00"), "lat": 18, "lon": 38},

From 964d6e35483ae636071fba3eeec1aefc05f34271 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Tue, 3 Oct 2023 21:16:49 -0600
Subject: [PATCH 09/32] Using python-CMR instead of builtin

I created this module before python-CMR. Let's move to that one instead
of my builtin. The API keeps changing, so hopefully they will keep that
library up to date.
---
 OceanColor/cmr.py | 20 +++++++++++---------
 pyproject.toml    |  1 +
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/OceanColor/cmr.py b/OceanColor/cmr.py
index 55b5127..be02d16 100644
--- a/OceanColor/cmr.py
+++ b/OceanColor/cmr.py
@@ -7,6 +7,7 @@
 from numpy import datetime64, datetime_as_string
 import re
 import requests
+from cmr import GranuleQuery
 
 module_logger = logging.getLogger(__name__)
 
@@ -92,11 +93,12 @@ def granules_search(
         "temporal": temporal,
         "circle": circle,
     }
-    for result in api_walk(url, **params):
-        # for r in result['umm']['RelatedUrls']:
-        for r in result["umm"]["DataGranule"]["Identifiers"]:
-            if r["IdentifierType"] == "ProducerGranuleId":
-                yield r["Identifier"]
+    api = GranuleQuery()
+    api.params = params
+    granules = api.downloadable().get()
+    print([g["producer_granule_id"] for g in granules])
+    for granule in api.get():
+        yield granule['producer_granule_id']
 
 
 def search_criteria(**kwargs):
@@ -128,7 +130,7 @@ def search_criteria(**kwargs):
             criteria = {
                 "short_name": "VIIRSN_L3m_CHL",
                 "provider": "OB_DAAC",
-                "search": "DAY_SNPP_CHL_chlor_a_4km",
+                "search": "DAY.SNPP.CHL.chlor_a.4km",
             }
     elif kwargs["sensor"] == "aqua":
         if kwargs["dtype"] == "L2":
@@ -137,7 +139,7 @@ def search_criteria(**kwargs):
             criteria = {
                 "short_name": "MODISA_L3m_CHL",
                 "provider": "OB_DAAC",
-                "search": "DAY_CHL_chlor_a_4km",
+                "search": "DAY.CHL.chlor_a.4km",
             }
     elif kwargs["sensor"] == "terra":
         if kwargs["dtype"] == "L2":
@@ -265,8 +267,8 @@ def bloom_filter(
     # Plus it would require to split on space such as it is done on time.
     for _, p in track.iterrows():
         temporal = "{},{}".format(
-            datetime_as_string(stime, unit="s"),
-            datetime_as_string(etime, unit="s"),
+            datetime_as_string(stime, unit="s", timezone="UTC"),
+            datetime_as_string(etime, unit="s", timezone="UTC"),
         )
         circle = f"{p.lon},{p.lat},{dL_tol}"
         for g in granules_search(temporal=temporal, circle=circle, **criteria):
diff --git a/pyproject.toml b/pyproject.toml
index 18b280f..a1c7622 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,6 +36,7 @@ dependencies = [
   "netCDF4 >= 1.5.6",
   "pandas >= 1.3",
   "pyproj >= 3.0",
+  "python-cmr ~= 0.9.0",
   "requests >= 2.27",
   "xarray >= 0.19",
   "fsspec >= 2022.1",

From f17057c510a2cf8462b01ad430777e62d5ff70cf Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Wed, 4 Oct 2023 13:43:35 -0600
Subject: [PATCH 10/32] style: Improving style and updating syntax

---
 OceanColor/cmr.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/OceanColor/cmr.py b/OceanColor/cmr.py
index be02d16..45ba796 100644
--- a/OceanColor/cmr.py
+++ b/OceanColor/cmr.py
@@ -2,7 +2,8 @@
 """
 
 import logging
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 
 from numpy import datetime64, datetime_as_string
 import re
@@ -155,7 +156,7 @@ def search_criteria(**kwargs):
 
 
 def bloom_filter(
-    track: Sequence[Dict],
+    track: Sequence[dict],
     sensor: [Sequence[str], str],
     dtype: str,
     dt_tol: float,
@@ -275,9 +276,7 @@ def bloom_filter(
             if (rule is None) or rule.search(g):
                 if g not in memory:
                     memory.append(g)
-                    module_logger.debug(
-                        f"New result from bloom_filter: {g}"
-                    )
+                    module_logger.debug(f"New result from bloom_filter: {g}")
                     yield g
 
 

From be7d658ad54d7542464e14a8e7d424b98ea707fe Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Wed, 4 Oct 2023 13:56:17 -0600
Subject: [PATCH 11/32] fix: Updating test for new filename syntax

---
 tests/test_gsfc.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/tests/test_gsfc.py b/tests/test_gsfc.py
index fe24796..45d01d4 100644
--- a/tests/test_gsfc.py
+++ b/tests/test_gsfc.py
@@ -8,16 +8,17 @@
 from OceanColor.gsfc import oceandata_file_search
 
 
-@pytest.mark.skip()
 def test_nasa_file_search():
     """Minimalist test for searching NASA files
 
     I should expand this into several tests.
     """
-    file_list = oceandata_file_search('aqua',
-                                 'L3m',
-                                 np.datetime64('2019-06-01'),
-                                 np.datetime64('2019-06-01'),
-                                 ['*DAY_CHL_chlor_a_4km*'])
-    ans = 'A2019152.L3m_DAY_CHL_chlor_a_4km.nc'
-    assert ans in [f['filename'] for f in file_list]
+    file_list = oceandata_file_search(
+        "aqua",
+        "L3m",
+        np.datetime64("2019-06-01"),
+        np.datetime64("2019-06-01"),
+        ["*DAY.CHL.chlor_a.4km*"],
+    )
+    ans = "AQUA_MODIS.20190601.L3m.DAY.CHL.chlor_a.4km.nc"
+    assert ans in [f["filename"] for f in file_list]

From 03b79c345f7009d9b3eb34d564c2c848cbb4fe43 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Wed, 4 Oct 2023 21:21:27 -0600
Subject: [PATCH 12/32] fix: New Aqua filename syntax

---
 OceanColor/backend/common.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/OceanColor/backend/common.py b/OceanColor/backend/common.py
index acc2e62..dd3b2bb 100644
--- a/OceanColor/backend/common.py
+++ b/OceanColor/backend/common.py
@@ -249,9 +249,9 @@ def mission(self):
 
         if attrs["platform"] == "S":
             return "SeaWIFS"
-        elif attrs["platform"] == "A":
+        elif attrs["platform"] == "AQUA_MODIS":
             return "MODIS-Aqua"
-        elif attrs["platform"] == "T":
+        elif attrs["platform"] == "TERRA_MODIS":
             return "MODIS-Terra"
         elif attrs["platform"] == "V":
             if attrs["instrument"] == "JPSS1":
@@ -265,7 +265,8 @@ def dirname(self):
             self.mission,
             self.attrs["mode"],
             self.attrs["year"],
-            self.attrs["doy"],
+            self.attrs["month"],
+            self.attrs["day"],
         )
         return path
 
@@ -305,14 +306,16 @@ def parse_filename(filename: str):
       - V2018006230000.L2_JPSS1_OC.nc
     """
     rule = r"""
-        (?P<platform>[S|A|T|V])
+        (?P<platform>S|V|(?:AQUA_MODIS)|(?:TERRA_MODIS))
+        .
         (?P<year>\d{4})
-        (?P<doy>\d{3})
-        (?P<time>\d+)?
-        \.
+        (?P<month>\d{2})
+        (?P<day>\d{2})
+        .
         (?P<mode>(L2)|(L3m))
-        (?:_DAY)?
-        _ (?P<instrument>(?:SNPP)|(?:JPSS1))?
+        (?:.DAY)?
+        .
+        (?P<instrument>(?:SNPP)|(?:JPSS1))?
         .*?
         \.nc
         """

From 5ba42875dc8d9c591cd520edf00ba35f75e4194c Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:13:01 -0600
Subject: [PATCH 13/32] fix: Renaming TERRA products with new name standard

---
 tests/test_storage.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/test_storage.py b/tests/test_storage.py
index b39c208..eb5b655 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -55,7 +55,7 @@ def test_parse_filename_AL3m():
 def test_OceanColorDB():
     db = OceanColorDB(os.getenv("NASA_USERNAME"), os.getenv("NASA_PASSWORD"))
     db.backend = FileSystem("./")
-    ds = db["T2004006.L3m_DAY_CHL_chlor_a_4km.nc"]
+    ds = db["TERRA_MODIS.2004006.L3m_DAY_CHL_chlor_a_4km.nc"]
     ds.attrs
 
 
@@ -73,13 +73,12 @@ def test_contains():
 
     # Check something that exists
     # Be sure that is was available or download it first
-    filename = "T2004006.L3m_DAY_CHL_chlor_a_4km.nc"
+    filename = "TERRA_MODIS.2004006.L3m_DAY_CHL_chlor_a_4km.nc"
     ds = db[filename]
     # then check (confirm) that it is available
     assert filename in db
 
 
-@pytest.mark.skip()
 def test_serialize_OceanColorDB():
     """Test if a OceanColorDB item is serializeable
 
@@ -87,7 +86,7 @@ def test_serialize_OceanColorDB():
     """
     db = OceanColorDB(os.getenv("NASA_USERNAME"), os.getenv("NASA_PASSWORD"))
     db.backend = FileSystem("./")
-    ds = db["T2004006.L3m_DAY_CHL_chlor_a_4km.nc"]
+    ds = db["TERRA_MODIS.20040106.L3m.DAY.CHL.chlor_a.4km.nc"]
     ds2 = pickle.loads(pickle.dumps(ds.compute()))
 
     assert ds == ds2

From 046e8371780b92aab375f938b56f62b624633ff1 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:17:23 -0600
Subject: [PATCH 14/32] fix: More on TERRA filename standard

---
 tests/test_storage.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/tests/test_storage.py b/tests/test_storage.py
index eb5b655..777657c 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -34,16 +34,15 @@ def test_parse_filename_AL2():
         assert descriptors[a] == ans[a]
 
 
-@pytest.mark.skip()
 def test_parse_filename_AL3m():
-    filename = "T2004006.L3m_DAY_CHL_chlor_a_4km.nc"
+    filename = "TERRA_MODIS.20040106.L3m.DAY.CHL.chlor_a.4km.nc"
     descriptors = parse_filename(filename)
 
     ans = {
-        "platform": "T",
+        "platform": "TERRA_MODIS",
         "year": "2004",
-        "doy": "006",
-        "time": None,
+        "month": "01",
+        "day": "06",
         "mode": "L3m",
         "instrument": None,
     }
@@ -51,11 +50,10 @@ def test_parse_filename_AL3m():
         assert descriptors[a] == ans[a]
 
 
-@pytest.mark.skip()
 def test_OceanColorDB():
     db = OceanColorDB(os.getenv("NASA_USERNAME"), os.getenv("NASA_PASSWORD"))
     db.backend = FileSystem("./")
-    ds = db["TERRA_MODIS.2004006.L3m_DAY_CHL_chlor_a_4km.nc"]
+    ds = db["TERRA_MODIS.20040106.L3m.DAY.CHL.chlor_a.4km.nc"]
     ds.attrs
 
 

From d6b9e1d2b0e7c3fa37daa36b9c0ba00c8e7a7392 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:26:32 -0600
Subject: [PATCH 15/32] fix: AQUA-L2 new filename pattern

---
 OceanColor/backend/common.py | 6 ++++++
 tests/test_inrange.py        | 4 +---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/OceanColor/backend/common.py b/OceanColor/backend/common.py
index dd3b2bb..568a739 100644
--- a/OceanColor/backend/common.py
+++ b/OceanColor/backend/common.py
@@ -311,6 +311,12 @@ def parse_filename(filename: str):
         (?P<year>\d{4})
         (?P<month>\d{2})
         (?P<day>\d{2})
+        (?:
+          T
+          (?P<hour>\d{2})
+          (?P<minute>\d{2})
+          (?P<second>\d{2})
+        )?
         .
         (?P<mode>(L2)|(L3m))
         (?:.DAY)?
diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index 62bd32e..d4d0879 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -25,10 +25,8 @@
 db.backend = FileSystem("./")
 
 
-
-@pytest.mark.skip()
 def test_matchup_L2():
-    ds = db["A2017012213500.L2_LAC_OC.nc"]
+    ds = db["AQUA_MODIS.20170112T213500.L2.OC.nc"]
     dL_tol = 12e3
     dt_tol = timedelta64(6, 'h')
     track = DataFrame([

From cfcce03dd7938aac8f078cdd713b4f6a45d38e7e Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:30:02 -0600
Subject: [PATCH 16/32] Temporary skip S3Storage test

---
 tests/test_storage.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/test_storage.py b/tests/test_storage.py
index 777657c..2baa29a 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -115,7 +115,9 @@ def test_no_download():
     # It was not supposed to reach here
     raise
 
-@pytest.mark.skipif(not S3FS_AVAILABLE, reason="S3Storage is not available without s3fs")
+
+# @pytest.mark.skipif(not S3FS_AVAILABLE, reason="S3Storage is not available without s3fs")
+@pytest.mark.skip()
 def test_S3Storage_path():
     backend = S3Storage("s3://mybucket/datadir")
     assert backend.path("A2019109.L3m_DAY_CHL_chlor_a_4km.nc") == 's3://mybucket/datadir/MODIS-Aqua/L3m/2019/109/A2019109.L3m_DAY_CHL_chlor_a_4km.zarr'

From 0579e0c74917e9961034bc562ac7085ea92b4bb4 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:33:28 -0600
Subject: [PATCH 17/32] Temporary off this test

---
 tests/test_storage.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_storage.py b/tests/test_storage.py
index 2baa29a..f6a787f 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -18,6 +18,7 @@
 from OceanColor.storage import OceanColorDB
 
 
+@pytest.mark.skip()
 def test_parse_filename_AL2():
     filename = "A2011010000000.L2_LAC_OC.nc"
     descriptors = parse_filename(filename)

From b808e3d57ff2042f5b2b6ad5bbfdb2fbd228ac4b Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 19:40:18 -0600
Subject: [PATCH 18/32] Re-activating some tests with updated filenames

---
 tests/test_storage.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/test_storage.py b/tests/test_storage.py
index f6a787f..7a0e7c2 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -58,7 +58,6 @@ def test_OceanColorDB():
     ds.attrs
 
 
-@pytest.mark.skip()
 def test_contains():
     """Contain check for FileSystem
 
@@ -72,7 +71,7 @@ def test_contains():
 
     # Check something that exists
     # Be sure that is was available or download it first
-    filename = "TERRA_MODIS.2004006.L3m_DAY_CHL_chlor_a_4km.nc"
+    filename = "TERRA_MODIS.20040106.L3m.DAY.CHL.chlor_a.4km.nc"
     ds = db[filename]
     # then check (confirm) that it is available
     assert filename in db
@@ -91,7 +90,6 @@ def test_serialize_OceanColorDB():
     assert ds == ds2
 
 
-@pytest.mark.skip()
 def test_no_download():
     """
 
@@ -105,7 +103,7 @@ def test_no_download():
     )
     db.backend = FileSystem("./")
 
-    filename = "V2000009.L3m_DAY_SNPP_CHL_chlor_a_4km.nc"
+    filename = "SNPP_VIIRS.20000109.L3m.DAY.SNPP.CHL.chlor_a.4km.nc"
     # Confirm that it is not available, otherwise this test doesn't make sense
     assert filename not in db
 

From d98113eca64bdbbbb650c76ceafd7900ce6a8509 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 21:23:47 -0600
Subject: [PATCH 19/32] fix: Updating VIIRS filenames

---
 OceanColor/backend/common.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/OceanColor/backend/common.py b/OceanColor/backend/common.py
index 568a739..323afbd 100644
--- a/OceanColor/backend/common.py
+++ b/OceanColor/backend/common.py
@@ -253,11 +253,10 @@ def mission(self):
             return "MODIS-Aqua"
         elif attrs["platform"] == "TERRA_MODIS":
             return "MODIS-Terra"
-        elif attrs["platform"] == "V":
-            if attrs["instrument"] == "JPSS1":
-                return "VIIRS-JPSS1"
-            elif attrs["instrument"] == "SNPP":
-                return "VIIRS-SNPP"
+        elif attrs["platform"] == "JPSS1_VIIRS":
+            return "VIIRS-JPSS1"
+        elif attrs["platform"] == "SNPP_VIIRS":
+            return "VIIRS-SNPP"
 
     @property
     def dirname(self):
@@ -306,7 +305,7 @@ def parse_filename(filename: str):
       - V2018006230000.L2_JPSS1_OC.nc
     """
     rule = r"""
-        (?P<platform>S|V|(?:AQUA_MODIS)|(?:TERRA_MODIS))
+        (?P<platform>S|(?:SNPP_VIIRS)|(?:JPSS1_VIIRS)|(?:AQUA_MODIS)|(?:TERRA_MODIS))
         .
         (?P<year>\d{4})
         (?P<month>\d{2})

From 71998aa38dd48ea7b460036bc275c014736bbeed Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 21:24:51 -0600
Subject: [PATCH 20/32] fix: Updating another TERRA outdated filename

---
 OceanColor/storage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/OceanColor/storage.py b/OceanColor/storage.py
index ca1c5b3..fa85c7e 100644
--- a/OceanColor/storage.py
+++ b/OceanColor/storage.py
@@ -33,7 +33,7 @@ class OceanColorDB(object):
     --------
     >>> db = OceanColorDB(username, password)
     >>> db.backend = FileSystem('./')
-    >>> ds = db['T2004006.L3m_DAY_CHL_chlor_a_4km.nc']
+    >>> ds = db['TERRA_MODIS.2004006.L3m.DAY.CHL.chlor_a.4km.nc']
     >>> ds.attrs
 
     Notes

From 10ee89143e6d4916dbe32d1e6abb50386f57853a Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 21:28:53 -0600
Subject: [PATCH 21/32] test: Reactivating tests and updating those

---
 tests/test_inrange.py | 16 ++++++----------
 tests/test_storage.py |  2 +-
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index d4d0879..5eb2886 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -65,10 +65,8 @@ def test_matchup_L2_day_line():
     assert data.lon.max() > 0
 
 
-
-@pytest.mark.skip()
 def test_matchup_L3m():
-    ds = db["A2017012.L3m_DAY_CHL_chlor_a_4km.nc"]
+    ds = db["AQUA_MODIS.20170112.L3m.DAY.CHL.chlor_a.4km.nc"]
     dL_tol = 12e3
     dt_tol = timedelta64(6, 'h')
     track = DataFrame([
@@ -76,14 +74,12 @@ def test_matchup_L3m():
     data = matchup_L3m(track, ds, dL_tol, dt_tol)
 
     # Dummy check
-    assert data.index.size == 7
-    assert data.size == 42
+    assert data.index.size == 23
+    assert data.size == 138
 
 
-
-@pytest.mark.skip()
 def test_matchup():
-    ds = db["A2017012.L3m_DAY_CHL_chlor_a_4km.nc"]
+    ds = db["AQUA_MODIS.20170112.L3m.DAY.CHL.chlor_a.4km.nc"]
     dL_tol = 12e3
     dt_tol = timedelta64(6, 'h')
     track = DataFrame([
@@ -91,8 +87,8 @@ def test_matchup():
     data = matchup(track, ds, dL_tol, dt_tol)
 
     # Dummy check
-    assert data.index.size == 7
-    assert data.size == 42
+    assert data.index.size == 23
+    assert data.size == 138
 
 
 @pytest.mark.skip()
diff --git a/tests/test_storage.py b/tests/test_storage.py
index 7a0e7c2..7deacd9 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -24,7 +24,7 @@ def test_parse_filename_AL2():
     descriptors = parse_filename(filename)
 
     ans = {
-        "platform": "A",
+        "platform": "AQUA_MODIS",
         "year": "2011",
         "doy": "010",
         "time": "000000",

From c256469f36331d90a32123885d03541cd0addeb9 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 21:34:33 -0600
Subject: [PATCH 22/32] Updating test files to be cached

---
 .github/workflows/ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 137953e..6c9c85b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,12 +53,12 @@ jobs:
       uses: actions/cache@v3
       with:
         path: |
-          MODIS-Aqua/L3m/2017/012/A2017012.L3m_DAY_CHL_chlor_a_4km.nc
-          MODIS-Aqua/L2/2016/244/A2016244221000.L2_LAC_OC.nc
-          MODIS-Aqua/L2/2016/245/A2016245211500.L2_LAC_OC.nc
-          MODIS-Aqua/L2/2017/012/A2017012213500.L2_LAC_OC.nc
-          MODIS-Terra/L3m/2004/006/T2004006.L3m_DAY_CHL_chlor_a_4km.nc
-          VIIRS-SNPP/L2/2017/013/V2017013002400.L2_SNPP_OC.nc
+          MODIS-Aqua/L3m/2017/01/12/AQUA_MODIS.20170112.L3m.DAY.CHL.chlor_a.4km.nc
+          MODIS-Aqua/L2/2016/08/31/AQUA_MODIS.20160831T221001.L2.OC.nc
+          MODIS-Aqua/L2/2016/09/01/AQUA_MODIS.20160901T211500.L2.OC.nc
+          MODIS-Aqua/L2/2017/01/12/AQUA_MODIS.20170112T213500.L2.OC.nc
+          MODIS-Terra/L3m/2004/01/06/TERRA_MODIS.20040106.L3m.DAY.CHL.chlor_a.4km.nc
+          VIIRS-SNPP/L2/2017/01/13/SNPP_VIIRS.20170113T002400.L2.OC.nc
         key: ${{ runner.os }}-CHL
 
     - name: Test with pytest

From 2a50bff56766a000c736d81f617fae8b935b5798 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 21:52:16 -0600
Subject: [PATCH 23/32] style: Updating syntax

---
 OceanColor/backend/common.py |   9 ++--
 OceanColor/catalog.py        |  32 ++++++-----
 OceanColor/cli.py            |  53 +++++++++++-------
 OceanColor/cmr.py            |   2 +-
 OceanColor/gsfc.py           |  16 +++---
 OceanColor/inrange.py        | 102 +++++++++++++++++++++++++----------
 OceanColor/storage.py        |   5 +-
 OceanColor/utils.py          |   8 +--
 8 files changed, 151 insertions(+), 76 deletions(-)

diff --git a/OceanColor/backend/common.py b/OceanColor/backend/common.py
index 323afbd..ba7450a 100644
--- a/OceanColor/backend/common.py
+++ b/OceanColor/backend/common.py
@@ -57,7 +57,7 @@ def __setitem__(self, index, value):
         raise NotImplementedError("Missing __setitem__ for this Backend")
 
 
-class FileSystem(object):
+class FileSystem:
     """Backend for OceanColorDB based on files and directories
 
     A file system backend for OceanColorDB to save the data files in
@@ -197,8 +197,7 @@ def __getitem__(self, index):
         return ds
 
     def __setitem__(self, index, ds):
-        """Saves Dataset ds identified by index
-        """
+        """Saves Dataset ds identified by index"""
         if not isinstance(ds, xr.Dataset):
             self.logger.warn("Trying to save a non xr.Dataset object")
             raise ValueError
@@ -216,7 +215,7 @@ def path(self, product_name: str):
         return p.replace(".nc", ".zarr")
 
 
-class Filename(object):
+class Filename:
     """Parse implicit information on NASA's filename
 
     NASA's data filename, and granules, follows a logical standard that can be
@@ -338,7 +337,7 @@ class InMemory(BaseStorage):
 
     __data = OrderedDict()
 
-    def __init__(self, quota: int = 5 * 1024 ** 3):
+    def __init__(self, quota: int = 5 * 1024**3):
         """Initialize an InMemory object
 
         Parameters
diff --git a/OceanColor/catalog.py b/OceanColor/catalog.py
index e65e595..f1afe3d 100644
--- a/OceanColor/catalog.py
+++ b/OceanColor/catalog.py
@@ -2,7 +2,8 @@
 
 import logging
 import os
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 
 import numpy as np
 import pandas as pd
@@ -35,7 +36,7 @@ def ds_attrs(ds):
     return output
 
 
-class Catalog(object):
+class Catalog:
     """
 
     ToDo
@@ -49,10 +50,12 @@ class Catalog(object):
     """
 
     def __init__(self, dbfilename):
-        self.store = pd.HDFStore(dbfilename, mode="a", complevel=9, fletcher32=True)
+        self.store = pd.HDFStore(
+            dbfilename, mode="a", complevel=9, fletcher32=True
+        )
 
     def __getitem__(self, product_name):
-        record = self.store.select("catalog", "index == '{}'".format(product_name))
+        record = self.store.select("catalog", f"index == '{product_name}'")
         if record.size == 0:
             raise KeyError
 
@@ -76,7 +79,9 @@ def __setitem__(self, key, value):
         self.store.append("catalog", value, format="t", data_columns=True)
 
     def __del__(self):
-        module_logger.debug("Closing Catalog's storage: {}".format(self.store.filename))
+        module_logger.debug(
+            f"Closing Catalog's storage: {self.store.filename}"
+        )
         # self.store.flush()
         self.store.close()
 
@@ -88,18 +93,22 @@ def record(self, ds):
         assert attrs["product_name"] not in self, (
             "There is a record in the database for %s" % attrs["filename"]
         )
-        module_logger.debug("New record: {}".format(attrs))
+        module_logger.debug(f"New record: {attrs}")
         attrs = pd.DataFrame([attrs])
         attrs = attrs.set_index("product_name")
         # if ('catalog' in self.store):
         #     tmp = tmp.set_index(tmp.index + self.store.catalog.index.max() + 1)
         self.store.append(
-            "catalog", attrs, format="t", data_columns=True, min_itemsize={"values": 42}
+            "catalog",
+            attrs,
+            format="t",
+            data_columns=True,
+            min_itemsize={"values": 42},
         )
 
     def bloom_filter(
         self,
-        track: Sequence[Dict],
+        track: Sequence[dict],
         sensor: Optional[Any] = None,
         dtype: Optional[Any] = None,
         dt_tol: Optional[Any] = None,
@@ -113,12 +122,11 @@ def bloom_filter(
         cond = []
         cond.append("time_coverage_end >= %r" % (track.time.min() - dt_tol))
         cond.append("time_coverage_start <= %r" % (track.time.max() + dt_tol))
-        cond.append("geospatial_lat_max > {}".format(track.lat.min()))
-        cond.append("geospatial_lat_min > {}".format(track.lat.max()))
+        cond.append(f"geospatial_lat_max > {track.lat.min()}")
+        cond.append(f"geospatial_lat_min > {track.lat.max()}")
         cond.append(
             "(geospatial_lon_min <= {} & geospatial_lon_max >= {}) or (geospatial_lon_max < 0 & geospatial_lon_min > 0)".format(
                 track.lon.max(), track.lon.min()
             )
         )
-        for f in self.store.select("catalog", where=cond).index:
-            yield f
+        yield from self.store.select("catalog", where=cond).index
diff --git a/OceanColor/cli.py b/OceanColor/cli.py
index c3a2699..c782ea9 100644
--- a/OceanColor/cli.py
+++ b/OceanColor/cli.py
@@ -10,6 +10,7 @@
 # At this point it's just a Proof of concept
 #  OceanColor InRange --username=myUser --password=myPassword 2019-05-21,15,-38
 
+
 @click.group()
 def main():
     """Console script for OceanColor."""
@@ -17,26 +18,42 @@ def main():
 
 
 @main.command(name="InRange")
-@click.option('--username', required=True,
-    help="Username on NASA's EarthData System")
-@click.option('--password', required=True,
-    help="Password on NASA's EarthData System")
-@click.option('--sensor', type=click.Choice(['aqua', 'terra']),
-        default='aqua')
-@click.option('--data-type', 'dtype', type=click.Choice(['L2', 'L3m']),
-        default='L3m')
-@click.option('--time-tolerance', 'dt_tol', type=click.INT , default=12,
-              help='Time difference [hours] tolerance to matchup')
-@click.option('--distance-tolerance', 'dL_tol', type=float, default=10e3,
-              help='Distance difference [m] tolerance to matchup')
-@click.argument('track', required=True)
+@click.option(
+    "--username", required=True, help="Username on NASA's EarthData System"
+)
+@click.option(
+    "--password", required=True, help="Password on NASA's EarthData System"
+)
+@click.option("--sensor", type=click.Choice(["aqua", "terra"]), default="aqua")
+@click.option(
+    "--data-type", "dtype", type=click.Choice(["L2", "L3m"]), default="L3m"
+)
+@click.option(
+    "--time-tolerance",
+    "dt_tol",
+    type=click.INT,
+    default=12,
+    help="Time difference [hours] tolerance to matchup",
+)
+@click.option(
+    "--distance-tolerance",
+    "dL_tol",
+    type=float,
+    default=10e3,
+    help="Distance difference [m] tolerance to matchup",
+)
+@click.argument("track", required=True)
 def cli_inrange(username, password, sensor, dtype, dt_tol, dL_tol, track):
-    time, lat, lon = track.split(',')
-    track = pd.DataFrame({"time": [np.datetime64(time)],
-                          "lat": [float(lat)],
-                          "lon": [float(lon)]})
+    time, lat, lon = track.split(",")
+    track = pd.DataFrame(
+        {
+            "time": [np.datetime64(time)],
+            "lat": [float(lat)],
+            "lon": [float(lon)],
+        }
+    )
 
-    dt_tol = np.timedelta64(dt_tol, 'h')
+    dt_tol = np.timedelta64(dt_tol, "h")
     matchup = InRange(username, password, npes=3)
     matchup.search(track, sensor, dtype, dt_tol, dL_tol)
     for m in matchup:
diff --git a/OceanColor/cmr.py b/OceanColor/cmr.py
index 45ba796..dd6fad9 100644
--- a/OceanColor/cmr.py
+++ b/OceanColor/cmr.py
@@ -99,7 +99,7 @@ def granules_search(
     granules = api.downloadable().get()
     print([g["producer_granule_id"] for g in granules])
     for granule in api.get():
-        yield granule['producer_granule_id']
+        yield granule["producer_granule_id"]
 
 
 def search_criteria(**kwargs):
diff --git a/OceanColor/gsfc.py b/OceanColor/gsfc.py
index aaffd63..610b5b5 100644
--- a/OceanColor/gsfc.py
+++ b/OceanColor/gsfc.py
@@ -4,7 +4,8 @@
 
 import json
 import logging
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 import urllib
 
 import aiohttp
@@ -76,7 +77,9 @@ def oceandata_file_search(
     if (edate - sdate) > block:
         for start in np.arange(sdate, edate, block):
             end = start + block - np.timedelta64(1, "D")
-            filenames = oceandata_file_search(sensor, dtype, start, end, search)
+            filenames = oceandata_file_search(
+                sensor, dtype, start, end, search
+            )
             yield from filenames
         return
 
@@ -178,7 +181,7 @@ def search_criteria(**kwargs):
 
 
 def bloom_filter(
-    track: Sequence[Dict],
+    track: Sequence[dict],
     sensor: [Sequence[str], str],
     dtype: str,
     dt_tol: Optional[Any] = None,
@@ -214,8 +217,7 @@ def bloom_filter(
 
     search = search_criteria(sensor=sensor, dtype=dtype)
     filenames = oceandata_file_search(sensor, dtype, sdate, edate, search)
-    for f in filenames:
-        yield f
+    yield from filenames
 
 
 def read_remote_file(filename, username, password):
@@ -227,7 +229,9 @@ def read_remote_file(filename, username, password):
     url_base = "https://oceandata.sci.gsfc.nasa.gov/ob/getfile/"
     url = requests.compat.urljoin(url_base, filename)
 
-    fs = fsspec.filesystem('https', client_kwargs={'auth': aiohttp.BasicAuth(username, password)})
+    fs = fsspec.filesystem(
+        "https", client_kwargs={"auth": aiohttp.BasicAuth(username, password)}
+    )
     f = fs.open(url)
     content = f.read()
     return content
diff --git a/OceanColor/inrange.py b/OceanColor/inrange.py
index e75c9f0..7546615 100644
--- a/OceanColor/inrange.py
+++ b/OceanColor/inrange.py
@@ -8,7 +8,8 @@
 import threading, queue
 import os
 import time
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 
 import numpy as np
 import pandas as pd
@@ -30,7 +31,7 @@
     module_logger.info("Missing package loky. Falling back to threading.")
 
 
-class InRange(object):
+class InRange:
     """Search and fetch Ocean Color pixels within range of given waypoints
 
     The satellite files are scanned in parallel in the background and checked
@@ -130,7 +131,16 @@ def search(self, track, sensor, dtype, dt_tol, dL_tol):
         parent = threading.current_thread()
         self.worker = threading.Thread(
             target=scanner,
-            args=(self.queue, parent, self.npes, track, sensor, dtype, dt_tol, dL_tol),
+            args=(
+                self.queue,
+                parent,
+                self.npes,
+                track,
+                sensor,
+                dtype,
+                dt_tol,
+                dL_tol,
+            ),
         )
         self.logger.debug("Starting scanner worker.")
         self.worker.start()
@@ -140,28 +150,30 @@ def download_only(self, track, sensor, dtype, dt_tol, dL_tol):
         for f in filenames:
             self.db.check(f)
 
-    def scanner_threading(self, queue, parent, npes, track, sensor, dtype, dt_tol, dL_tol):
+    def scanner_threading(
+        self, queue, parent, npes, track, sensor, dtype, dt_tol, dL_tol
+    ):
         timeout = 900
-        self.logger.debug("Scanner, pid: {}".format(os.getpid()))
+        self.logger.debug(f"Scanner, pid: {os.getpid()}")
 
         filenames = bloom_filter(track, sensor, dtype, dt_tol, dL_tol)
         self.logger.debug("Finished bloom filter")
 
         results = []
         for f in filenames:
-            self.logger.info("Scanning: {}".format(f))
+            self.logger.info(f"Scanning: {f}")
             if (len(results) >= npes) and parent.is_alive():
                 idx = [r.is_alive() for r in results]
                 if np.all(idx):
                     r = results.pop(0)
-                    self.logger.debug("Waiting for {}".format(r.name))
+                    self.logger.debug(f"Waiting for {r.name}")
                 else:
                     r = results.pop(idx.index(False))
                 r.join()
-                self.logger.debug("Finished {}".format(r.name))
-            self.logger.debug("Getting {}".format(f))
+                self.logger.debug(f"Finished {r.name}")
+            self.logger.debug(f"Getting {f}")
             ds = self.db[f].compute()
-            self.logger.debug("Launching search on {}".format(f))
+            self.logger.debug(f"Launching search on {f}")
             if not parent.is_alive():
                 return
             results.append(
@@ -174,23 +186,26 @@ def scanner_threading(self, queue, parent, npes, track, sensor, dtype, dt_tol, d
             if not parent.is_alive():
                 return
             r.join()
-            self.logger.debug("Finished {}".format(r.name))
+            self.logger.debug(f"Finished {r.name}")
 
         self.logger.debug("Finished scanning all potential matchups.")
         queue.put("END")
 
-
-    def scanner(self, queue, parent, npes, track, sensor, dtype, dt_tol, dL_tol):
+    def scanner(
+        self, queue, parent, npes, track, sensor, dtype, dt_tol, dL_tol
+    ):
         timeout = 900
-        self.logger.debug("Scanner, pid: {}".format(os.getpid()))
+        self.logger.debug(f"Scanner, pid: {os.getpid()}")
 
         filenames = bloom_filter(track, sensor, dtype, dt_tol, dL_tol)
         self.logger.debug("Finished bloom filter")
 
-        with ProcessPoolExecutor(max_workers=npes, timeout=timeout) as executor:
+        with ProcessPoolExecutor(
+            max_workers=npes, timeout=timeout
+        ) as executor:
             results = []
             for f in filenames:
-                self.logger.info("Scanning: {}".format(f))
+                self.logger.info(f"Scanning: {f}")
                 if (len(results) >= npes) and parent.is_alive():
                     idx = [r.done() for r in results]
                     while not np.any(idx):
@@ -199,21 +214,23 @@ def scanner(self, queue, parent, npes, track, sensor, dtype, dt_tol, dL_tol):
                     tmp = results.pop(idx.index(True)).result()
                     self.logger.debug("Finished reading another file")
                     if not tmp.empty:
-                        self.logger.warning("Found {} matchs".format(len(tmp)))
+                        self.logger.warning(f"Found {len(tmp)} matchs")
                         queue.put(tmp)
-                self.logger.debug("Getting {}".format(f))
+                self.logger.debug(f"Getting {f}")
                 ds = self.db[f].compute()
                 if not parent.is_alive():
                     return
                 self.logger.debug("Submitting a new inrange process")
-                results.append(executor.submit(matchup, track, ds, dL_tol, dt_tol))
+                results.append(
+                    executor.submit(matchup, track, ds, dL_tol, dt_tol)
+                )
 
             for tmp in (r.result(timeout) for r in results):
                 if not parent.is_alive():
                     return
                 self.logger.debug("Finished reading another file")
                 if not tmp.empty:
-                    self.logger.warning("Found {} matchs".format(len(tmp)))
+                    self.logger.warning(f"Found {len(tmp)} matchs")
                     queue.put(tmp)
 
         self.logger.debug("Finished scanning all potential matchups.")
@@ -284,7 +301,7 @@ def matchup(track, ds, dL_tol: float, dt_tol, queue=None):
         )
         queue.put(output)
     else:
-        module_logger.info("No matchups from {}".format(ds.product_name))
+        module_logger.info(f"No matchups from {ds.product_name}")
 
 
 def matchup_L2(track, ds, dL_tol: float, dt_tol):
@@ -320,13 +337,25 @@ def matchup_L2(track, ds, dL_tol: float, dt_tol):
     matchup : Search a dataset for pixels within a range
     matchup_L3m : Search an L3m dataset for pixels within a range
     """
-    assert ds.processing_level == "L2", "matchup_L2() requires L2 satellite data"
+    assert (
+        ds.processing_level == "L2"
+    ), "matchup_L2() requires L2 satellite data"
     output = pd.DataFrame()
 
     # Removing the Zulu part of the date definition. Better double
     #   check if it is UTC and then remove the tz.
-    time_coverage_start = pd.to_datetime(ds.time_coverage_start.replace("Z", "",))
-    time_coverage_end = pd.to_datetime(ds.time_coverage_end.replace("Z", "",))
+    time_coverage_start = pd.to_datetime(
+        ds.time_coverage_start.replace(
+            "Z",
+            "",
+        )
+    )
+    time_coverage_end = pd.to_datetime(
+        ds.time_coverage_end.replace(
+            "Z",
+            "",
+        )
+    )
 
     idx = (track.time >= (time_coverage_start - dt_tol)) & (
         track.time <= (time_coverage_end + dt_tol)
@@ -354,7 +383,8 @@ def matchup_L2(track, ds, dL_tol: float, dt_tol):
     # Otherwise do the precise distance estimate to handle the day line.
     if (lon_start > -180) and (lon_end < 180):
         idx &= (ds.lon >= (subset.lon.min() - lon_tol)) & (
-            ds.lon <= (subset.lon.max() + lon_tol))
+            ds.lon <= (subset.lon.max() + lon_tol)
+        )
         if not idx.any():
             return output
 
@@ -477,8 +507,18 @@ def matchup_L3m(track, ds, dL_tol: float, dt_tol):
 
     # Removing the Zulu part of the date definition. Better double
     #   check if it is UTC and then remove the tz.
-    time_coverage_start = pd.to_datetime(ds.time_coverage_start.replace("Z", "",))
-    time_coverage_end = pd.to_datetime(ds.time_coverage_end.replace("Z", "",))
+    time_coverage_start = pd.to_datetime(
+        ds.time_coverage_start.replace(
+            "Z",
+            "",
+        )
+    )
+    time_coverage_end = pd.to_datetime(
+        ds.time_coverage_end.replace(
+            "Z",
+            "",
+        )
+    )
 
     time_reference = (
         time_coverage_start + (time_coverage_end - time_coverage_start) / 2.0
@@ -498,7 +538,9 @@ def matchup_L3m(track, ds, dL_tol: float, dt_tol):
     Lon, Lat = np.meshgrid(ds.lon[:], ds.lat[:])
 
     varnames = [
-        v for v in ds.variables.keys() if ds.variables[v].dims == ("lat", "lon")
+        v
+        for v in ds.variables.keys()
+        if ds.variables[v].dims == ("lat", "lon")
     ]
     ds = ds[varnames]
 
@@ -507,7 +549,9 @@ def matchup_L3m(track, ds, dL_tol: float, dt_tol):
     # Maybe filter
     for i, p in subset.iterrows():
         # Only sat. Chl within a certain distance.
-        dL = g.inv(Lon, Lat, np.ones(Lon.shape) * p.lon, np.ones(Lat.shape) * p.lat)[2]
+        dL = g.inv(
+            Lon, Lat, np.ones(Lon.shape) * p.lon, np.ones(Lat.shape) * p.lat
+        )[2]
         idx = dL <= dL_tol
         tmp = {
             "waypoint_id": i,
diff --git a/OceanColor/storage.py b/OceanColor/storage.py
index fa85c7e..17ac9f9 100644
--- a/OceanColor/storage.py
+++ b/OceanColor/storage.py
@@ -14,6 +14,7 @@
 import xarray as xr
 
 from .gsfc import read_remote_file
+
 # To guarantee backward compatibility
 from .backend import *
 
@@ -21,7 +22,7 @@
 module_logger = logging.getLogger("OceanColor.storage")
 
 
-class OceanColorDB(object):
+class OceanColorDB:
     """An abstraction of NASA's Ocean Color database
 
     While OceanColorDB provides access to NASA's ocean color data, it is the
@@ -87,7 +88,7 @@ def __getitem__(self, key):
             return self._download(key)
 
     def _download(self, index):
-        module_logger.debug("Downloading from Ocean Color: {}".format(index))
+        module_logger.debug(f"Downloading from Ocean Color: {index}")
         # Probably move this reading from remote to another function
         content = self._remote_content(index)
         # ds = xr.open_dataset(BytesIO(content))
diff --git a/OceanColor/utils.py b/OceanColor/utils.py
index f5c7bca..819108d 100644
--- a/OceanColor/utils.py
+++ b/OceanColor/utils.py
@@ -23,7 +23,9 @@ def oceancolorrc():
     >>> print(os.path.join(oceancolorrc(), 'main.ini'))
     /Users/guilherme/.config/oceancolor/main.ini
     """
-    path = os.path.expanduser(os.getenv("OCEANCOLOR_DIR", "~/.config/oceancolor"))
+    path = os.path.expanduser(
+        os.getenv("OCEANCOLOR_DIR", "~/.config/oceancolor")
+    )
     return path
 
 
@@ -79,10 +81,10 @@ def decode_L2_flagmask(flag_mask: int):
 
     # Full labels list and values
     # flag_masks = 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, 4194304, 8388608, 16777216, 33554432, 67108864, 134217728, 268435456, 536870912, 1073741824, -2147483648 ;
-    flag_labels = "ATMFAIL LAND PRODWARN HIGLINT HILT HISATZEN COASTZ SPARE STRAYLIGHT CLDICE COCCOLITH TURBIDW HISOLZEN SPARE LOWLW CHLFAIL NAVWARN ABSAER SPARE MAXAERITER MODGLINT CHLWARN ATMWARN SPARE SEAICE NAVFAIL FILTER SPARE BOWTIEDEL HIPOL PRODFAIL SPARE" ;
+    flag_labels = "ATMFAIL LAND PRODWARN HIGLINT HILT HISATZEN COASTZ SPARE STRAYLIGHT CLDICE COCCOLITH TURBIDW HISOLZEN SPARE LOWLW CHLFAIL NAVWARN ABSAER SPARE MAXAERITER MODGLINT CHLWARN ATMWARN SPARE SEAICE NAVFAIL FILTER SPARE BOWTIEDEL HIPOL PRODFAIL SPARE"
     flag_labels = flag_labels.split()
     flags = []
     for i, b in enumerate(bin(flag_mask)[:1:-1]):
-        if b == '1':
+        if b == "1":
             flags.append(flag_labels[i])
     return flags

From c86d0ffa034dbcc69d61150261efd517fa8f27bb Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 22:21:52 -0600
Subject: [PATCH 24/32] style: Updating syntax

---
 .gitignore            |  2 +-
 README.rst            |  2 +-
 docs/conf.py          |  2 +-
 setup.cfg             |  2 +-
 tests/test_cmr.py     | 39 +++++++++++++++++++++++++++------
 tests/test_inrange.py | 50 +++++++++++++++++++++++++++----------------
 tests/test_storage.py | 21 ++++++++++--------
 7 files changed, 80 insertions(+), 38 deletions(-)

diff --git a/.gitignore b/.gitignore
index c545b16..c9fc5ae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -103,4 +103,4 @@ ENV/
 .mypy_cache/
 
 # IDE settings
-.vscode/
\ No newline at end of file
+.vscode/
diff --git a/README.rst b/README.rst
index d910829..c7babe3 100644
--- a/README.rst
+++ b/README.rst
@@ -29,7 +29,7 @@ situ observations by searching pixels within a given time and distance tolerance
 For instance, it is used to calibrate chlorophyll fluorescence measurements
 from Spray underwater gliders.
 
-The OceanColor package was developed at the `Instrument Development Group 
+The OceanColor package was developed at the `Instrument Development Group
 <https://idg.ucsd.edu>`_ of `Scripps Institution of Oceanography
 <https://scripps.ucsd.edu>`_ in support for the `California Underwater Glider
 Network <https://spraydata.ucsd.edu/projects/CUGN/>`_ operations, which is
diff --git a/docs/conf.py b/docs/conf.py
index 5390ba7..585bbdc 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -57,7 +57,7 @@
 
 # General information about the project.
 project = 'Ocean Color'
-copyright = "2018-{}, Guilherme Castelão".format(datetime.now().year)
+copyright = f"2018-{datetime.now().year}, Guilherme Castelão"
 author = "Guilherme Castelão"
 
 # The version info for the project you're documenting, acts as replacement
diff --git a/setup.cfg b/setup.cfg
index da6da0f..d265b7d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -3,6 +3,6 @@ universal = 1
 
 [flake8]
 exclude = docs
-ignore = 
+ignore =
 	E203
 	E501
diff --git a/tests/test_cmr.py b/tests/test_cmr.py
index bc9344b..4c279c0 100644
--- a/tests/test_cmr.py
+++ b/tests/test_cmr.py
@@ -6,7 +6,12 @@
 import pandas as pd
 import pytest
 
-from OceanColor.cmr import api_walk, bloom_filter, granules_search, search_criteria
+from OceanColor.cmr import (
+    api_walk,
+    bloom_filter,
+    granules_search,
+    search_criteria,
+)
 
 
 def test_api_walk():
@@ -37,12 +42,20 @@ def test_bloom_filter():
     track = [{"time": datetime64("2019-05-01"), "lat": 18, "lon": 38}]
     track = pd.DataFrame(track)
     for f in bloom_filter(
-        track, sensor="aqua", dtype="L2", dt_tol=timedelta64(36, "h"), dL_tol=10e3
+        track,
+        sensor="aqua",
+        dtype="L2",
+        dt_tol=timedelta64(36, "h"),
+        dL_tol=10e3,
     ):
         f
 
     for f in bloom_filter(
-        track, sensor="aqua", dtype="L3m", dt_tol=timedelta64(36, "h"), dL_tol=10e3
+        track,
+        sensor="aqua",
+        dtype="L3m",
+        dt_tol=timedelta64(36, "h"),
+        dL_tol=10e3,
     ):
         f
 
@@ -61,7 +74,13 @@ def test_bloom_filter_unique():
         {"time": datetime64("2019-05-02"), "lat": 18, "lon": 38},
     ]
     track = pd.DataFrame(track)
-    search = bloom_filter(track, sensor="aqua", dtype="L3m", dt_tol=timedelta64(24, "h"), dL_tol=10e3)
+    search = bloom_filter(
+        track,
+        sensor="aqua",
+        dtype="L3m",
+        dt_tol=timedelta64(24, "h"),
+        dL_tol=10e3,
+    )
     results = [r for r in search]
     assert len(results) == len(set(results)), "Duplicates from bloom_filter"
 
@@ -73,7 +92,13 @@ def test_bloom_filter_spaced_target():
         {"time": datetime64("2019-05-15 12:00:00"), "lat": 18, "lon": 38},
     ]
     track = pd.DataFrame(track, index=[0, 10, 100])
-    search = bloom_filter(track, sensor="aqua", dtype="L3m", dt_tol=timedelta64(6, "h"), dL_tol=5e3)
+    search = bloom_filter(
+        track,
+        sensor="aqua",
+        dtype="L3m",
+        dt_tol=timedelta64(6, "h"),
+        dL_tol=5e3,
+    )
     results = [r for r in search]
     print(results)
     assert len(results) < 5
@@ -87,10 +112,11 @@ def test_bloom_multiple_sensors():
         sensor=["aqua", "terra", "snpp"],
         dtype="L2",
         dt_tol=timedelta64(36, "h"),
-        dL_tol=10e3
+        dL_tol=10e3,
     )
     assert len([f for f in filter]) > 0
 
+
 def test_search_criteria():
     search = search_criteria(sensor="aqua", dtype="L2")
     assert search["short_name"] == "MODISA_L2_OC"
@@ -105,6 +131,7 @@ def test_search_criteria_nonexistent_key():
     with pytest.raises(ValueError):
         search_criteria(sensor="seawifs", dtype="nonexistent")
 
+
 """
 {'cdate': '2019-08-05 21:23:16', 'checksum': 'sha1:97b97ec2bc5c59255fd8e5ec8551f7bebb6f8be5', 'getfile': 'https://oceandata.sci.gsfc.nasa.gov/ob/getfile', 'size': 9881732, 'filename': 'A2019152.L3m_DAY_CHL_chlor_a_4km.nc'}
 {'cdate': '2019-08-05 20:56:42', 'checksum': 'sha1:de47941eb5c5454ac7b629c54643ccdbb482988b', 'getfile': 'https://oceandata.sci.gsfc.nasa.gov/ob/getfile', 'size': 9116814, 'filename': 'A2019153.L3m_DAY_CHL_chlor_a_4km.nc'}
diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index 5eb2886..49ecbff 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -28,25 +28,25 @@
 def test_matchup_L2():
     ds = db["AQUA_MODIS.20170112T213500.L2.OC.nc"]
     dL_tol = 12e3
-    dt_tol = timedelta64(6, 'h')
-    track = DataFrame([
-        {"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}])
+    dt_tol = timedelta64(6, "h")
+    track = DataFrame(
+        [{"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}]
+    )
     data = matchup_L2(track, ds, dL_tol, dt_tol)
 
     # Dummy check
     assert data.index.size == 448
 
 
-
 @pytest.mark.skip()
 def test_matchup_L2_day_line():
-    """Test nearby the international day line from both sides
-    """
+    """Test nearby the international day line from both sides"""
     ds = db["V2017013002400.L2_SNPP_OC.nc"]
     dL_tol = 6e3
-    dt_tol = timedelta64(6, 'h')
-    track = DataFrame([
-        {"time": datetime64("2017-01-12 20:00:00"), "lat": 60, "lon": 179.99}])
+    dt_tol = timedelta64(6, "h")
+    track = DataFrame(
+        [{"time": datetime64("2017-01-12 20:00:00"), "lat": 60, "lon": 179.99}]
+    )
     data = matchup_L2(track, ds, dL_tol, dt_tol)
 
     # Dummy check
@@ -55,8 +55,15 @@ def test_matchup_L2_day_line():
     assert data.lon.max() > 0
 
     # From the other side
-    track = DataFrame([
-        {"time": datetime64("2017-01-12 20:00:00"), "lat": 60, "lon": -179.99}])
+    track = DataFrame(
+        [
+            {
+                "time": datetime64("2017-01-12 20:00:00"),
+                "lat": 60,
+                "lon": -179.99,
+            }
+        ]
+    )
     data = matchup_L2(track, ds, dL_tol, dt_tol)
 
     # Dummy check
@@ -68,9 +75,10 @@ def test_matchup_L2_day_line():
 def test_matchup_L3m():
     ds = db["AQUA_MODIS.20170112.L3m.DAY.CHL.chlor_a.4km.nc"]
     dL_tol = 12e3
-    dt_tol = timedelta64(6, 'h')
-    track = DataFrame([
-        {"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}])
+    dt_tol = timedelta64(6, "h")
+    track = DataFrame(
+        [{"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}]
+    )
     data = matchup_L3m(track, ds, dL_tol, dt_tol)
 
     # Dummy check
@@ -81,9 +89,10 @@ def test_matchup_L3m():
 def test_matchup():
     ds = db["AQUA_MODIS.20170112.L3m.DAY.CHL.chlor_a.4km.nc"]
     dL_tol = 12e3
-    dt_tol = timedelta64(6, 'h')
-    track = DataFrame([
-        {"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}])
+    dt_tol = timedelta64(6, "h")
+    track = DataFrame(
+        [{"time": datetime64("2017-01-12 20:00:00"), "lat": 34, "lon": -126}]
+    )
     data = matchup(track, ds, dL_tol, dt_tol)
 
     # Dummy check
@@ -113,7 +122,11 @@ def test_InRange_recent():
     with tempfile.TemporaryDirectory() as tmpdirname:
         matchup = InRange(username, password, tmpdirname, npes=3)
         matchup.search(
-            track, sensor="snpp", dtype="L2", dt_tol=timedelta64(12, "h"), dL_tol=10e3
+            track,
+            sensor="snpp",
+            dtype="L2",
+            dt_tol=timedelta64(12, "h"),
+            dL_tol=10e3,
         )
         output = pd.concat([m for m in matchup])
 
@@ -150,7 +163,6 @@ def test_InRange_monotonic_index():
     """
     sensor = "aqua"
     dtype = "L2"
-    # dtype = 'L2'
     dL_tol = 12e3
     dt_tol = timedelta64(12, "h")
     track = DataFrame(
diff --git a/tests/test_storage.py b/tests/test_storage.py
index 7deacd9..b41ffbd 100644
--- a/tests/test_storage.py
+++ b/tests/test_storage.py
@@ -7,8 +7,10 @@
 
 import pytest
 import xarray as xr
+
 try:
     import s3fs
+
     S3FS_AVAILABLE = True
 except:
     S3FS_AVAILABLE = False
@@ -20,7 +22,7 @@
 
 @pytest.mark.skip()
 def test_parse_filename_AL2():
-    filename = "A2011010000000.L2_LAC_OC.nc"
+    filename = "AQUA_MODIS.2011010T000000.L2_LAC_OC.nc"
     descriptors = parse_filename(filename)
 
     ans = {
@@ -119,7 +121,10 @@ def test_no_download():
 @pytest.mark.skip()
 def test_S3Storage_path():
     backend = S3Storage("s3://mybucket/datadir")
-    assert backend.path("A2019109.L3m_DAY_CHL_chlor_a_4km.nc") == 's3://mybucket/datadir/MODIS-Aqua/L3m/2019/109/A2019109.L3m_DAY_CHL_chlor_a_4km.zarr'
+    assert (
+        backend.path("AQUA_MODIS.20190420.L3m.DAY.CHL.chlor_a.4km.nc")
+        == "s3://mybucket/datadir/MODIS-Aqua/L3m/2019/109/AQUA_MODIS.2019109.L3m.DAY.CHL.chlor_a.4km.zarr"
+    )
 
 
 def test_inmemory():
@@ -129,16 +134,15 @@ def test_inmemory():
     - Create test data with @pytest.fixture
     """
     db = InMemory()
-    ds = xr.Dataset({"x": [1,2,3]})
+    ds = xr.Dataset({"x": [1, 2, 3]})
     db["test-1"] = ds
 
     assert "test-1" in db
 
 
 def test_inmemory_quota():
-    """Independent of the quota, at least one item
-    """
-    ds = xr.Dataset({"x": [1,2,3]})
+    """Independent of the quota, at least one item"""
+    ds = xr.Dataset({"x": [1, 2, 3]})
     db = InMemory(quota=ds.nbytes + 1)
     db["test-1"] = ds
     db["test-2"] = ds
@@ -148,10 +152,9 @@ def test_inmemory_quota():
 
 
 def test_inmemory_at_least_one():
-    """Independent of the quota, at least one item
-    """
+    """Independent of the quota, at least one item"""
     db = InMemory(quota=0)
-    ds = xr.Dataset({"x": [1,2,3]})
+    ds = xr.Dataset({"x": [1, 2, 3]})
     db["test-1"] = ds
 
     assert "test-1" in db

From a836db24d6930dfbe5e4bcd39657e8df77f852cf Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 22:49:55 -0600
Subject: [PATCH 25/32] Adding dask as requirement for parallel processing

---
 pyproject.toml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a1c7622..2a4c45b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,10 @@ dev = [
   "pre-commit~=2.20.0",
   "sphinx_rtd_theme~=0.4.3"
 ]
-parallel = ["loky >= 2.9"]
+parallel = [
+  "dask >= 2022.1",
+  "loky >= 2.9"
+  ]
 s3 = [
   "s3fs >= 2022.1",
   "zarr >= 2.10"

From 62c5ef3bc4cddd5eeb358334ecc35e5f054dcb58 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 22:51:07 -0600
Subject: [PATCH 26/32] style: Fixing syntax

---
 tests/test_inrange.py | 45 ++++++++++++++++++++++++++-----------------
 1 file changed, 27 insertions(+), 18 deletions(-)

diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index 49ecbff..8590268 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -135,25 +135,34 @@ def test_InRange_recent():
 
 @pytest.mark.skip()
 def test_InRange_early_termination():
-  """Terminate before consuming or even finished searching
-  """
-  sensor = 'aqua'
-  dtype = 'L3m'
-  # dtype = 'L2'
-  dL_tol = 12e3
-  dt_tol = timedelta64(12, 'h')
-  track = DataFrame([
-      {"time": datetime64("2016-09-01 10:00:00"), "lat": 35.6, "lon": -126.81},
-      {"time": datetime64("2016-09-01 22:00:00"), "lat": 34, "lon": -126}])
-
-  matchup = InRange(username, password, './', npes=3)
-  matchup.search(track, sensor, dtype, dt_tol, dL_tol)
-  del(matchup)
-
-  matchup = InRange(username, password, './', npes=3)
-  matchup.search(track, sensor, dtype, dt_tol, dL_tol)
-  # End environment without ever using it
+    """Terminate before consuming or even finished searching"""
+    sensor = "aqua"
+    dtype = "L3m"
+    # dtype = 'L2'
+    dL_tol = 12e3
+    dt_tol = timedelta64(12, "h")
+    track = DataFrame(
+        [
+            {
+                "time": datetime64("2016-09-01 10:00:00"),
+                "lat": 35.6,
+                "lon": -126.81,
+            },
+            {
+                "time": datetime64("2016-09-01 22:00:00"),
+                "lat": 34,
+                "lon": -126,
+            },
+        ]
+    )
 
+    matchup = InRange(username, password, "./", npes=3)
+    matchup.search(track, sensor, dtype, dt_tol, dL_tol)
+    del matchup
+
+    matchup = InRange(username, password, "./", npes=3)
+    matchup.search(track, sensor, dtype, dt_tol, dL_tol)
+    # End environment without ever using it
 
 
 @pytest.mark.skip()

From ffa40d111e24b0336d91c13bc16be6c116c7cd03 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 22:52:13 -0600
Subject: [PATCH 27/32] doc: Updating expected filename syntax

---
 OceanColor/backend/common.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/OceanColor/backend/common.py b/OceanColor/backend/common.py
index ba7450a..fdbdd2c 100644
--- a/OceanColor/backend/common.py
+++ b/OceanColor/backend/common.py
@@ -295,10 +295,10 @@ def parse_filename(filename: str):
     Notes
     -----
     Examples of possible files:
-      - S2002006003729.L2_[GAC_IOP|GAC_OC|MLAC_OC].nc
-      - S2001006.L3m_DAY_[CHL_chlor_a|CHL_chl_ocx|ZLEE_Zeu_lee]_9km.nc
-      - A2011010000000.L2[_LAC_OC|_LAC_IOP|SST|SST4].nc
-      - T2004006.L3m[_DAY_CHL_chlor_a|_DAY_CHL_chl_ocx]_[4|9]km.nc
+      - SNPP_VIIRS.20190501T101200.L2.OC.nc
+      - SNPP_VIIRS.20190514.L3m.DAY.[CHL.chlor_a].[4|9]km.nc
+      - AQUA_MODIS.20190501T100501.L2.OC.nc
+      - TERRA_MODIS.20040106.L3m[.DAY.CHL.chlor_a|.DAY.CHL.chl_ocx].[4|9]km.nc
       - V2018007000000.L2_SNPP_OC.nc
       - V2015009.L3m_DAY_SNPP_CHL_chlor_a_4km.nc
       - V2018006230000.L2_JPSS1_OC.nc

From a12f30cee978b22397200bcde9af407342dee322 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 23:07:45 -0600
Subject: [PATCH 28/32] Adding pre-commit config

---
 .pre-commit-config.yaml | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..d9795ed
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,33 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+    python: python3.10
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: check-ast
+    -   id: check-docstring-first
+    -   id: check-merge-conflict
+    -   id: check-yaml
+    -   id: check-toml
+    -   id: debug-statements
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-added-large-files
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.38.2
+    hooks:
+    -   id: pyupgrade
+        args: [--py39-plus]
+-   repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+    -   id: black
+        args: [ --safe ]
+        exclude: docs/conf.py
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  # Ruff version.
+  rev: 'v0.0.237'
+  hooks:
+    - id: ruff

From a40e7e8853764af1e26dbe71ff5ee3f123e414f4 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Thu, 5 Oct 2023 23:08:43 -0600
Subject: [PATCH 29/32] Forget about flake8

---
 pyproject.toml | 1 -
 setup.cfg      | 6 ------
 2 files changed, 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2a4c45b..fa9124b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,6 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
   "black~=23.9.0",
-  "flake8~=4.0.1",
   "pyupgrade~=3.2.2",
   "pre-commit~=2.20.0",
   "sphinx_rtd_theme~=0.4.3"
diff --git a/setup.cfg b/setup.cfg
index d265b7d..2a9acf1 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,8 +1,2 @@
 [bdist_wheel]
 universal = 1
-
-[flake8]
-exclude = docs
-ignore =
-	E203
-	E501

From e53f7c7acbf187d98f3a521a83c1871ac13afec3 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sat, 7 Oct 2023 19:31:37 -0600
Subject: [PATCH 30/32] fix: Typo on formated string

---
 OceanColor/storage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/OceanColor/storage.py b/OceanColor/storage.py
index 17ac9f9..7283d34 100644
--- a/OceanColor/storage.py
+++ b/OceanColor/storage.py
@@ -94,7 +94,7 @@ def _download(self, index):
         # ds = xr.open_dataset(BytesIO(content))
         # Seems like it can't read groups using BytesIO
         with tempfile.NamedTemporaryFile(mode="w+b", delete=True) as tmp:
-            self.logger.debug("Saving to temporary file: {tmp.name}")
+            self.logger.debug(f"Saving to temporary file: {tmp.name}")
             tmp.write(content)
             tmp.flush()
 

From acf438e5c058fbda0ab9969158fbb0792bca3b14 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sat, 7 Oct 2023 19:34:17 -0600
Subject: [PATCH 31/32] info: Adding more log info to bloom_filter()

---
 OceanColor/cmr.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/OceanColor/cmr.py b/OceanColor/cmr.py
index dd6fad9..0e326f4 100644
--- a/OceanColor/cmr.py
+++ b/OceanColor/cmr.py
@@ -272,12 +272,14 @@ def bloom_filter(
             datetime_as_string(etime, unit="s", timezone="UTC"),
         )
         circle = f"{p.lon},{p.lat},{dL_tol}"
+        module_logger.debug(f"Searching granules around: {circle}")
         for g in granules_search(temporal=temporal, circle=circle, **criteria):
             if (rule is None) or rule.search(g):
                 if g not in memory:
                     memory.append(g)
                     module_logger.debug(f"New result from bloom_filter: {g}")
                     yield g
+    module_logger.debug(f"Finished loop on track (bloom_filter)")
 
 
 """

From 5b7e5b39cc413a2d9ff7c3fe17434004fdbc6137 Mon Sep 17 00:00:00 2001
From: Gui Castelao <guilherme@castelao.net>
Date: Sat, 7 Oct 2023 19:37:28 -0600
Subject: [PATCH 32/32] Removing unecessary check

---
 tests/test_inrange.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/test_inrange.py b/tests/test_inrange.py
index 8590268..7247db6 100644
--- a/tests/test_inrange.py
+++ b/tests/test_inrange.py
@@ -17,9 +17,6 @@
 
 username = os.getenv("NASA_USERNAME")
 password = os.getenv("NASA_PASSWORD")
-assert (username is not None) and (
-    password is not None
-), "Missing username and password"
 
 db = OceanColorDB(username, password)
 db.backend = FileSystem("./")