diff --git a/.github/workflows/get_pypi_stats.yml b/.github/workflows/get_pypi_stats.yml index bd553e5be..0e5af599a 100644 --- a/.github/workflows/get_pypi_stats.yml +++ b/.github/workflows/get_pypi_stats.yml @@ -23,15 +23,14 @@ jobs: # Calculates pypi stats and clones and stores in CSV file - name: Update pypi stats files run: | - pip install -r requirements.txt + pip install -r requirements.txt pypistats python ./doc/source/tracking/pypistats/get_pypi_stats.py # Commits files to repository - name: Commit changes - uses: EndBug/add-and-commit@v7 + uses: EndBug/add-and-commit@v8 with: author_name: learn2phoenix message: "Pypi stats auto-update" add: "./doc/source/tracking/pypistats/*" -# add: "./pypistats/*" - branch: "traffic" # commits to branch "traffic" \ No newline at end of file +# add: "./pypistats/*" \ No newline at end of file diff --git a/.github/workflows/traffic_action.yml b/.github/workflows/traffic_action.yml index 52c3cafb0..0c5b3581b 100644 --- a/.github/workflows/traffic_action.yml +++ b/.github/workflows/traffic_action.yml @@ -35,10 +35,9 @@ jobs: # Commits files to repository - name: Commit changes - uses: EndBug/add-and-commit@v7 + uses: EndBug/add-and-commit@v8 with: author_name: Jessica Scheick message: "GitHub traffic auto-update" add: "./doc/source/tracking/traffic/*" # add: "./traffic/*" - branch: "traffic" # commits to branch "traffic" diff --git a/.github/workflows/uml_action.yml b/.github/workflows/uml_action.yml index 2eac90b64..b97bd9b7c 100644 --- a/.github/workflows/uml_action.yml +++ b/.github/workflows/uml_action.yml @@ -11,6 +11,8 @@ jobs: steps: - name: Check out repository uses: actions/checkout@v2 + with: + ref: ${{ github.event.pull_request.head.ref }} - name: set up environment run: | pip install -r requirements.txt @@ -23,9 +25,8 @@ jobs: rm ./packages_dev_uml.svg mv ./*.svg ./doc/source/user_guide/documentation/ - name: Commit changes - uses: EndBug/add-and-commit@v7 + uses: EndBug/add-and-commit@v8 with: author_name: GitHub Action message: "GitHub action UML generation auto-update" add: "./doc/source/user_guide/documentation/*" - ref: git branch --show-current diff --git a/doc/source/example_notebooks/IS2_data_read-in.ipynb b/doc/source/example_notebooks/IS2_data_read-in.ipynb index 6537777de..836381698 100644 --- a/doc/source/example_notebooks/IS2_data_read-in.ipynb +++ b/doc/source/example_notebooks/IS2_data_read-in.ipynb @@ -426,7 +426,7 @@ "\n", "***ATTENTION: icepyx loads your data by creating an Xarray DataSet for each input granule and then merging them. In some cases, the automatic merge fails and needs to be handled manually. In these cases, icepyx will return a warning with the error message from the failed Xarray merge and a list of per-granule DataSets***\n", "\n", - "This can happen if you unintentionally provide the same granule multiple times with different filenames." + "This can happen if you unintentionally provide the same granule multiple times with different filenames or in segmented products where the rgt+cycle automatically generated `gran_idx` values match. In this latter case, you can simply provide unique `gran_idx` values for each DataSet in `ds` and run `import xarray as xr` and `ds_merged = xr.merge(ds)` to create one merged DataSet." ] }, { diff --git a/doc/source/tracking/pypistats/downloads.svg b/doc/source/tracking/pypistats/downloads.svg index e95d220ee..ccc029a76 100644 --- a/doc/source/tracking/pypistats/downloads.svg +++ b/doc/source/tracking/pypistats/downloads.svg @@ -1,23 +1,23 @@ - + - + - 2021-12-03T10:07:24.089207 + 2022-03-17T21:02:01.353153 image/svg+xml - Matplotlib v3.4.2, https://matplotlib.org/ + Matplotlib v3.5.1, https://matplotlib.org/ - + @@ -26,34 +26,34 @@ L 720 144 L 720 0 L 0 0 z -" style="fill:none;"/> +" style="fill: #ffffff"/> - +" style="fill: #ffffff"/> - +" style="stroke: #000000; stroke-width: 0.8"/> - + - + - - + - + - + - + - + +" transform="scale(0.015625)"/> - - - - - - - - - + + + + + + + + + - + - + - +" transform="scale(0.015625)"/> - - - - - - - - - + + + + + + + + + - + - + - - - - - - - - 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without_mirrors,2021-06-29,10 -without_mirrors,2021-10-29,10 -without_mirrors,2021-11-02,10 -with_mirrors,2021-10-13,9 -with_mirrors,2021-11-10,9 without_mirrors,2021-06-07,9 without_mirrors,2021-06-20,9 without_mirrors,2021-07-16,9 without_mirrors,2021-07-30,9 without_mirrors,2021-08-04,9 -without_mirrors,2021-10-28,9 -without_mirrors,2021-11-10,9 -without_mirrors,2021-11-19,9 with_mirrors,2021-06-12,8 with_mirrors,2021-07-12,8 with_mirrors,2021-07-13,8 @@ -175,8 +449,6 @@ with_mirrors,2021-07-27,8 with_mirrors,2021-08-27,8 with_mirrors,2021-09-13,8 with_mirrors,2021-09-14,8 -with_mirrors,2021-09-27,8 -with_mirrors,2021-10-05,8 without_mirrors,2021-06-10,8 without_mirrors,2021-06-15,8 without_mirrors,2021-06-23,8 @@ -185,27 +457,16 @@ without_mirrors,2021-07-14,8 without_mirrors,2021-07-19,8 without_mirrors,2021-07-20,8 without_mirrors,2021-08-13,8 -without_mirrors,2021-10-02,8 -without_mirrors,2021-11-13,8 with_mirrors,2021-06-14,7 with_mirrors,2021-07-04,7 with_mirrors,2021-08-30,7 with_mirrors,2021-09-06,7 -with_mirrors,2021-11-21,7 without_mirrors,2021-06-06,7 without_mirrors,2021-06-08,7 without_mirrors,2021-07-23,7 without_mirrors,2021-09-06,7 -without_mirrors,2021-09-30,7 -without_mirrors,2021-10-01,7 -without_mirrors,2021-10-05,7 -without_mirrors,2021-11-11,7 -without_mirrors,2021-11-14,7 -without_mirrors,2021-11-18,7 -without_mirrors,2021-11-21,7 with_mirrors,2021-06-28,6 with_mirrors,2021-09-01,6 -with_mirrors,2021-11-09,6 without_mirrors,2021-06-09,6 without_mirrors,2021-06-12,6 without_mirrors,2021-07-02,6 @@ -214,16 +475,10 @@ without_mirrors,2021-07-08,6 without_mirrors,2021-07-15,6 without_mirrors,2021-07-27,6 without_mirrors,2021-09-01,6 -without_mirrors,2021-09-29,6 -without_mirrors,2021-11-08,6 -without_mirrors,2021-11-09,6 with_mirrors,2021-07-03,5 with_mirrors,2021-08-19,5 with_mirrors,2021-08-25,5 with_mirrors,2021-09-07,5 -with_mirrors,2021-10-19,5 -with_mirrors,2021-10-23,5 -with_mirrors,2021-11-06,5 without_mirrors,2021-06-14,5 without_mirrors,2021-07-03,5 without_mirrors,2021-07-04,5 @@ -233,23 +488,12 @@ without_mirrors,2021-08-24,5 without_mirrors,2021-09-04,5 without_mirrors,2021-09-05,5 without_mirrors,2021-09-07,5 -without_mirrors,2021-09-21,5 -without_mirrors,2021-09-27,5 -without_mirrors,2021-10-09,5 -without_mirrors,2021-10-19,5 -without_mirrors,2021-10-22,5 -without_mirrors,2021-10-23,5 -without_mirrors,2021-11-06,5 with_mirrors,2021-06-17,4 -with_mirrors,2021-11-07,4 without_mirrors,2021-06-13,4 without_mirrors,2021-06-24,4 without_mirrors,2021-07-05,4 without_mirrors,2021-08-11,4 without_mirrors,2021-09-15,4 -without_mirrors,2021-09-25,4 -without_mirrors,2021-10-06,4 -without_mirrors,2021-11-07,4 with_mirrors,2021-07-24,3 with_mirrors,2021-08-08,3 with_mirrors,2021-08-17,3 @@ -273,19 +517,11 @@ without_mirrors,2021-08-23,3 without_mirrors,2021-09-09,3 without_mirrors,2021-09-10,3 without_mirrors,2021-09-11,3 -without_mirrors,2021-10-13,3 -without_mirrors,2021-10-15,3 -without_mirrors,2021-10-25,3 without_mirrors,2021-11-24,3 with_mirrors,2021-08-09,2 with_mirrors,2021-08-14,2 with_mirrors,2021-08-15,2 with_mirrors,2021-08-18,2 -with_mirrors,2021-09-17,2 -with_mirrors,2021-09-18,2 -with_mirrors,2021-09-24,2 -with_mirrors,2021-10-07,2 -with_mirrors,2021-10-10,2 without_mirrors,2021-06-05,2 without_mirrors,2021-06-17,2 without_mirrors,2021-06-27,2 @@ -305,17 +541,6 @@ without_mirrors,2021-09-03,2 without_mirrors,2021-09-13,2 without_mirrors,2021-09-14,2 without_mirrors,2021-09-16,2 -without_mirrors,2021-09-17,2 -without_mirrors,2021-09-18,2 -without_mirrors,2021-09-19,2 -without_mirrors,2021-09-24,2 -without_mirrors,2021-09-28,2 -without_mirrors,2021-10-07,2 -without_mirrors,2021-10-10,2 -without_mirrors,2021-10-11,2 -without_mirrors,2021-10-16,2 -without_mirrors,2021-10-17,2 -without_mirrors,2021-10-21,2 with_mirrors,2021-09-08,1 without_mirrors,2021-06-19,1 without_mirrors,2021-07-24,1 @@ -327,9 +552,6 @@ without_mirrors,2021-08-29,1 without_mirrors,2021-08-31,1 without_mirrors,2021-09-08,1 without_mirrors,2021-09-12,1 -without_mirrors,2021-09-22,1 -without_mirrors,2021-09-26,1 -without_mirrors,2021-10-20,1 with_mirrors,2021-05-14,130 with_mirrors,2021-03-30,119 with_mirrors,2021-05-13,111 diff --git a/doc/source/tracking/pypistats/get_pypi_stats.py b/doc/source/tracking/pypistats/get_pypi_stats.py index 81dbbb995..c5340e448 100644 --- a/doc/source/tracking/pypistats/get_pypi_stats.py +++ b/doc/source/tracking/pypistats/get_pypi_stats.py @@ -4,31 +4,39 @@ cwd = os.getcwd() -trackpath = f'{cwd}/doc/source/tracking/pypistats/' +trackpath = f"{cwd}/doc/source/tracking/pypistats/" downloadfn = "downloads_data.csv" sysdownloadfn = "sys_downloads_data.csv" -downloads = pypistats.overall("icepyx", format="pandas").drop(columns=['percent']) +downloads = pypistats.overall("icepyx", total=True, format="pandas").drop( + columns=["percent"] +) downloads = downloads[downloads.category != "Total"] # try: exist_downloads = pd.read_csv(trackpath + downloadfn) # .drop(columns=['percent']) # exist_downloads = exist_downloads[exist_downloads.category != "Total"] -dl_data = downloads.merge(exist_downloads, how='outer', - on=['category', 'date', 'downloads']).reindex() +dl_data = downloads.merge( + exist_downloads, how="outer", on=["category", "date", "downloads"] +).reindex() # except: # dl_data = downloads dl_data.to_csv(trackpath + downloadfn, index=False) -sysdownloads = pypistats.system("icepyx", format="pandas").drop(columns=['percent']) +sysdownloads = pypistats.system("icepyx", total=True, format="pandas").drop( + columns=["percent"] +) sysdownloads = sysdownloads[sysdownloads.category != "Total"] # try: -exist_sysdownloads = pd.read_csv(trackpath + sysdownloadfn) # .drop(columns=['percent']) +exist_sysdownloads = pd.read_csv( + trackpath + sysdownloadfn +) # .drop(columns=['percent']) # exist_sysdownloads = exist_sysdownloads[exist_sysdownloads.category != "Total"] -exist_sysdownloads['category'] = exist_sysdownloads['category'].fillna("null") -sysdl_data = sysdownloads.merge(exist_sysdownloads, how='outer', - on=['category', 'date', 'downloads']).reindex() +exist_sysdownloads["category"] = exist_sysdownloads["category"].fillna("null") +sysdl_data = sysdownloads.merge( + exist_sysdownloads, how="outer", on=["category", "date", "downloads"] +).reindex() # except: # dl_data = sysdownloads @@ -36,6 +44,7 @@ dl_data = dl_data.groupby("category").get_group("without_mirrors").sort_values("date") -chart = dl_data.plot(x="date", y="downloads", figsize=(10, 2), - label="Number of PyPI Downloads") +chart = dl_data.plot( + x="date", y="downloads", figsize=(10, 2), label="Number of PyPI Downloads" +) chart.figure.savefig(trackpath + "downloads.svg") diff --git a/doc/source/tracking/pypistats/sys_downloads_data.csv b/doc/source/tracking/pypistats/sys_downloads_data.csv index 28657f828..95ebd07ae 100644 --- a/doc/source/tracking/pypistats/sys_downloads_data.csv +++ b/doc/source/tracking/pypistats/sys_downloads_data.csv @@ -1,67 +1,419 @@ category,date,downloads +null,2022-03-10,64 +null,2022-02-21,60 +null,2022-03-07,47 +null,2022-02-22,40 +null,2022-03-02,38 +null,2021-12-04,37 +null,2022-03-04,37 null,2021-09-20,32 -null,2021-06-30,21 -null,2021-07-26,20 +null,2022-03-15,26 +null,2021-12-02,25 +null,2021-12-08,24 +null,2021-12-09,24 +null,2022-03-13,24 +null,2022-03-01,23 +null,2021-12-16,21 +null,2022-01-10,20 +null,2022-02-20,20 Linux,2021-10-03,19 +null,2021-12-01,19 +null,2022-02-27,19 +null,2022-03-08,19 Linux,2021-10-04,18 -null,2021-07-25,17 -null,2021-08-06,16 null,2021-10-08,16 null,2021-10-27,16 -null,2021-07-17,15 -null,2021-08-12,15 null,2021-11-16,15 -Linux,2021-08-16,14 -Linux,2021-07-29,12 -null,2021-06-11,12 +null,2022-01-21,13 +null,2022-03-05,13 Linux,2021-10-31,11 Linux,2021-11-03,11 Linux,2021-11-04,11 Linux,2021-11-05,11 Linux,2021-11-15,11 +Linux,2021-11-25,11 +null,2022-02-26,11 Linux,2021-10-30,10 -null,2021-06-29,10 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-Linux,2021-10-26,5 -Linux,2021-11-11,5 -Linux,2021-11-21,5 null,2021-07-04,5 null,2021-07-23,5 -null,2021-11-12,5 -Windows,2021-11-22,5 Linux,2021-06-12,4 Linux,2021-06-13,4 Linux,2021-06-24,4 @@ -69,13 +421,6 @@ Linux,2021-07-14,4 Linux,2021-09-05,4 Linux,2021-09-06,4 Linux,2021-09-07,4 -Linux,2021-09-27,4 -Linux,2021-10-23,4 -Linux,2021-10-27,4 -Linux,2021-10-28,4 -Linux,2021-11-01,4 -Linux,2021-11-08,4 -Linux,2021-11-18,4 null,2021-06-07,4 null,2021-06-08,4 null,2021-07-02,4 @@ -83,10 +428,7 @@ null,2021-07-05,4 null,2021-07-20,4 null,2021-07-27,4 null,2021-08-01,4 -null,2021-10-26,4 -null,2021-10-30,4 Windows,2021-08-06,4 -Windows,2021-09-30,4 Darwin,2021-07-01,3 Linux,2021-06-07,3 Linux,2021-06-09,3 @@ -96,13 +438,6 @@ Linux,2021-07-15,3 Linux,2021-08-12,3 Linux,2021-08-22,3 Linux,2021-08-24,3 -Linux,2021-09-21,3 -Linux,2021-09-29,3 -Linux,2021-10-06,3 -Linux,2021-11-06,3 -Linux,2021-11-07,3 -Linux,2021-11-16,3 -Linux,2021-11-24,3 null,2021-06-06,3 null,2021-07-08,3 null,2021-07-14,3 @@ -111,14 +446,7 @@ null,2021-07-16,3 null,2021-07-22,3 null,2021-09-01,3 null,2021-09-11,3 -null,2021-10-09,3 -null,2021-10-22,3 -null,2021-10-28,3 -null,2021-11-04,3 Windows,2021-09-10,3 -Windows,2021-09-20,3 -Windows,2021-11-04,3 -Windows,2021-11-17,3 Windows,2021-11-23,3 Darwin,2021-08-19,2 Linux,2021-06-06,2 @@ -138,12 +466,6 @@ Linux,2021-09-04,2 Linux,2021-09-13,2 Linux,2021-09-14,2 Linux,2021-09-15,2 -Linux,2021-09-25,2 -Linux,2021-10-10,2 -Linux,2021-10-11,2 -Linux,2021-10-15,2 -Linux,2021-10-19,2 -Linux,2021-10-22,2 null,2021-06-05,2 null,2021-06-12,2 null,2021-06-18,2 @@ -157,13 +479,6 @@ null,2021-08-08,2 null,2021-08-20,2 null,2021-08-30,2 null,2021-09-04,2 -null,2021-09-18,2 -null,2021-09-25,2 -null,2021-09-30,2 -null,2021-10-13,2 -null,2021-10-19,2 -null,2021-11-02,2 -null,2021-11-19,2 Windows,2021-06-07,2 Windows,2021-06-11,2 Windows,2021-06-14,2 @@ -180,17 +495,6 @@ Windows,2021-08-21,2 Windows,2021-09-06,2 Windows,2021-09-15,2 Windows,2021-09-16,2 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620.650952 249.326699 +L 621.643658 249.326699 +L 622.636364 249.862584 +L 622.636364 249.862584 +" clip-path="url(#p59de5f1589)" style="fill: none; stroke: #ff7f0e; stroke-width: 1.5; stroke-linecap: square"/> - + - + @@ -2707,13 +3116,13 @@ z - + - + @@ -2741,10 +3150,10 @@ L 119 183.296562 - + - + diff --git a/doc/source/tracking/traffic/views.csv b/doc/source/tracking/traffic/views.csv index 114f086b7..d1ea92ece 100644 --- a/doc/source/tracking/traffic/views.csv +++ b/doc/source/tracking/traffic/views.csv @@ -309,7 +309,6 @@ _date,total_views,unique_views 2021-08-26,11,3 2021-08-27,8,4 2021-08-28,6,2 -2021-08-29,34,5 2021-08-29,35,6 2021-08-30,89,7 2021-08-31,58,12 @@ -415,4 +414,92 @@ _date,total_views,unique_views 2021-12-11,17,6 2021-12-12,14,6 2021-12-13,82,12 -2021-12-14,35,6 +2021-12-14,162,12 +2021-12-15,65,8 +2021-12-16,55,10 +2021-12-17,32,6 +2021-12-18,70,5 +2021-12-19,11,5 +2021-12-20,130,14 +2021-12-21,60,8 +2021-12-22,45,5 +2021-12-23,35,4 +2021-12-24,34,9 +2021-12-25,19,1 +2021-12-26,11,2 +2021-12-27,23,4 +2021-12-28,12,4 +2021-12-29,4,3 +2021-12-30,9,5 +2021-12-31,10,3 +2022-01-02,19,6 +2022-01-03,128,27 +2022-01-04,81,17 +2022-01-05,37,10 +2022-01-06,33,8 +2022-01-07,8,6 +2022-01-08,4,4 +2022-01-09,1,1 +2022-01-10,31,9 +2022-01-11,57,9 +2022-01-12,40,11 +2022-01-13,121,22 +2022-01-14,19,5 +2022-01-15,22,1 +2022-01-16,4,2 +2022-01-17,16,5 +2022-01-18,47,14 +2022-01-19,27,4 +2022-01-20,37,7 +2022-01-21,23,13 +2022-01-22,5,3 +2022-01-23,7,3 +2022-01-24,121,7 +2022-01-25,119,15 +2022-01-26,60,12 +2022-01-27,16,8 +2022-01-28,129,10 +2022-01-29,19,4 +2022-01-30,60,5 +2022-01-31,146,14 +2022-02-01,52,10 +2022-02-02,157,18 +2022-02-03,199,20 +2022-02-04,72,18 +2022-02-05,5,3 +2022-02-06,8,1 +2022-02-07,206,15 +2022-02-08,161,22 +2022-02-09,105,15 +2022-02-10,102,20 +2022-02-11,272,32 +2022-02-12,30,9 +2022-02-13,24,10 +2022-02-14,129,17 +2022-02-15,97,18 +2022-02-16,35,14 +2022-02-17,42,12 +2022-02-18,96,15 +2022-02-19,16,8 +2022-02-20,8,4 +2022-02-21,98,16 +2022-02-22,60,15 +2022-02-23,107,14 +2022-02-24,74,19 +2022-02-25,133,17 +2022-02-26,46,16 +2022-02-27,14,5 +2022-02-28,111,23 +2022-03-01,88,23 +2022-03-02,75,30 +2022-03-03,91,18 +2022-03-04,247,18 +2022-03-05,105,8 +2022-03-06,40,11 +2022-03-07,343,15 +2022-03-08,191,23 +2022-03-09,101,13 +2022-03-10,40,11 +2022-03-11,46,10 +2022-03-12,30,10 +2022-03-13,17,8 diff --git a/doc/source/user_guide/changelog/index.rst b/doc/source/user_guide/changelog/index.rst index bf7adce0f..2be70fa22 100644 --- a/doc/source/user_guide/changelog/index.rst +++ b/doc/source/user_guide/changelog/index.rst @@ -6,9 +6,17 @@ icepyx ChangeLog This is the list of changes made to icepyx in between each release. Full details can be found in the `commit logs `_. -Latest Release (Version 0.6.0) +Latest Release (Version 0.6.2) ------------------------------ +.. toctree:: + :maxdepth: 2 + + v0.6.2 + +Version 0.6.0 + 0.6.1 +--------------------- + .. toctree:: :maxdepth: 2 diff --git a/doc/source/user_guide/changelog/v0.6.0.rst b/doc/source/user_guide/changelog/v0.6.0.rst index fb481a0a6..795eab261 100644 --- a/doc/source/user_guide/changelog/v0.6.0.rst +++ b/doc/source/user_guide/changelog/v0.6.0.rst @@ -3,9 +3,14 @@ What's new in 0.6.0 (4 March 2022) ----------------------------------- -These are the changes in icepyx 0.6.0 See :ref:`release` for a full changelog +These are the changes in icepyx 0.6.0 (0.6.1) See :ref:`release` for a full changelog including other versions of icepyx. +Release 0.6.0 turned into release 0.6.1 due to a tagging + timing issue where the last pull request +was merged after the tag was created. +Increasing the version to 0.6.1 enabled us to quickly troubleshoot and fix our available builds, +but a new release log was not created. + New Features ~~~~~~~~~~~~ diff --git a/doc/source/user_guide/changelog/v0.6.2.rst b/doc/source/user_guide/changelog/v0.6.2.rst new file mode 100644 index 000000000..30b500998 --- /dev/null +++ b/doc/source/user_guide/changelog/v0.6.2.rst @@ -0,0 +1,28 @@ +.. _whatsnew_062: + +What's new in 0.6.2 (17 March 2022) +----------------------------------- + +These are the changes in icepyx 0.6.2. See :ref:`release` for a full changelog +including other versions of icepyx. + + +Bug fixes +~~~~~~~~~ + +- debug behind login Travis CI tests (#291) +- manually remove 'z' from datetime string (#294) + + +Maintenance +^^^^^^^^^^^ + +- update action add-and-commit v8 and remove branch/ref keywords (#290) +- add read-in functionality for deeply nested variables (e.g. ATL08) (#281) +- icepyx tracking (traffic and pypi) updates (#295) + + +Contributors +~~~~~~~~~~~~ + +.. contributors:: v0.6.0..v0.6.2|HEAD diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 7d6011125..47fd6e0d6 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - + classes_dev_uml - + icepyx.core.Earthdata.Earthdata @@ -29,17 +29,17 @@ icepyx.core.query.GenQuery - -GenQuery - -_end : datetime -_geom_filepath : NoneType -_spat_extent -_start : datetime -extent_type : str - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_end : datetime +_geom_filepath : NoneType +_spat_extent +_start : datetime +extent_type : str + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() @@ -58,104 +58,104 @@ icepyx.core.query.Query - -Query - -CMRparams -_CMRparams -_about_product -_cust_options : dict -_cycles : list -_email -_file_vars -_granules -_order_vars -_prod : NoneType, str -_readable_granule_name : list -_reqparams -_s3login_credentials -_session : Session -_source : str -_subsetparams : NoneType -_tracks : list -_version -cycles -dataset -dates -end_time -file_vars -granules -order_vars -product -product_version -reqparams -spatial_extent -start_time -tracks - -__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, files) -__str__() -avail_granules(ids, cycles, tracks, s3urls) -download_granules(path, verbose, subset, restart) -earthdata_login(uid, email, s3token) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +_CMRparams +_about_product +_cust_options : dict +_cycles : list +_email +_file_vars +_granules +_order_vars +_prod : str, NoneType +_readable_granule_name : list +_reqparams +_s3login_credentials +_session : Session +_source : str +_subsetparams : NoneType +_tracks : list +_version +cycles +dataset +dates +end_time +file_vars +granules +order_vars +product +product_version +reqparams +spatial_extent +start_time +tracks + +__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, files) +__str__() +avail_granules(ids, cycles, tracks, s3urls) +download_granules(path, verbose, subset, restart) +earthdata_login(uid, email, s3token) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams() +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - -__init__() + +Icesat2Data + + +__init__() icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + @@ -180,136 +180,137 @@ icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - + + _CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - + + _reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.core.read.Read - -Read - -_catalog_path : NoneType -_filelist : list, NoneType -_is2catalog : Catalog -_out_obj : Dataset -_pattern : str -_prod : NoneType, str -_read_vars -_source_type : str -data_source : NoneType -is2catalog -vars - -__init__(data_source, product, filename_pattern, catalog, out_obj_type) -_add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) -_build_dataset_template(file) -_build_single_file_dataset(file, groups_list) -_check_source_for_pattern(source, filename_pattern) -_read_single_var(file, grp_path) -load() + +Read + +_catalog_path : NoneType +_filelist : NoneType, list +_is2catalog : Catalog +_out_obj : Dataset +_pattern : str +_prod : str, NoneType +_read_vars +_source_type : str +data_source : NoneType +is2catalog +vars + +__init__(data_source, product, filename_pattern, catalog, out_obj_type) +_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) +_build_dataset_template(file) +_build_single_file_dataset(file, groups_list) +_check_source_for_pattern(source, filename_pattern) +_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) +_read_single_grp(file, grp_path) +load() icepyx.core.variables.Variables - -Variables - -_avail : list, NoneType -_session : NoneType -_vartype -_version : NoneType -path : NoneType -product : NoneType -wanted : NoneType, dict - -__init__(vartype, avail, wanted, session, product, version, path) -_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) -_get_combined_list(beam_list, keyword_list) -_get_sum_varlist(var_list, all_vars, defaults) -_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) -_iter_vars(sum_varlist, req_vars, vgrp) -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered) -remove(all, var_list, beam_list, keyword_list) + +Variables + +_avail : list, NoneType +_session : NoneType +_vartype +_version : NoneType +path : NoneType +product : NoneType +wanted : NoneType, dict + +__init__(vartype, avail, wanted, session, product, version, path) +_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) +_get_combined_list(beam_list, keyword_list) +_get_sum_varlist(var_list, all_vars, defaults) +_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) +_iter_vars(sum_varlist, req_vars, vgrp) +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) icepyx.core.variables.Variables->icepyx.core.query.Query - - + + _order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - + + _order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - + + _file_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - + + _read_vars icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): -query_icesat2_filelist(): tuple -request_OA_data(paras): -viz_elevation(): + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : str, NoneType +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): +query_icesat2_filelist(): tuple +request_OA_data(paras): +viz_elevation(): diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index 4d439940c..ce6608bb3 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,253 +4,253 @@ - + classes_user_uml - + icepyx.core.Earthdata.Earthdata - -Earthdata - + +Earthdata + capability_url email netrc : NoneType -pswd : NoneType, str +pswd : str, NoneType session : Session uid - + login(attempts) icepyx.core.query.GenQuery - -GenQuery - -extent_type : str - - + +GenQuery + +extent_type : str + + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -download(verbose, path, session, restart) -get_avail(CMRparams, reqparams) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, session, geom_filepath) + +Granules + +avail : list +orderIDs : list + +download(verbose, path, session, restart) +get_avail(CMRparams, reqparams) +place_order(CMRparams, reqparams, subsetparams, verbose, subset, session, geom_filepath) icepyx.core.query.Query - -Query - -CMRparams -cycles -dataset -dates -end_time -file_vars -granules -order_vars -product -product_version -reqparams -spatial_extent -start_time -tracks - -avail_granules(ids, cycles, tracks, s3urls) -download_granules(path, verbose, subset, restart) -earthdata_login(uid, email, s3token) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +cycles +dataset +dates +end_time +file_vars +granules +order_vars +product +product_version +reqparams +spatial_extent +start_time +tracks + +avail_granules(ids, cycles, tracks, s3urls) +download_granules(path, verbose, subset, restart) +earthdata_login(uid, email, s3token) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams() +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - + +Icesat2Data + + + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + icepyx.core.APIformatting.Parameters - -Parameters - -fmted_keys -partype -poss_keys - -build_params() -check_req_values() -check_values() + +Parameters + +fmted_keys +partype +poss_keys + +build_params() +check_req_values() +check_values() icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.core.read.Read - -Read - -data_source : NoneType -is2catalog -vars - -load() + +Read + +data_source : NoneType +is2catalog +vars + +load() icepyx.core.variables.Variables - -Variables - -path : NoneType -product : NoneType -wanted : NoneType, dict - -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered) -remove(all, var_list, beam_list, keyword_list) + +Variables + +path : NoneType +product : NoneType +wanted : NoneType, dict + +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - -_file_vars + + +_file_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : str, NoneType -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): -query_icesat2_filelist(): tuple -request_OA_data(paras): -viz_elevation(): + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): +query_icesat2_filelist(): tuple +request_OA_data(paras): +viz_elevation(): diff --git a/icepyx/core/Earthdata.py b/icepyx/core/Earthdata.py index cdf1f3382..b0c5ff6f3 100644 --- a/icepyx/core/Earthdata.py +++ b/icepyx/core/Earthdata.py @@ -129,7 +129,7 @@ def login(self, attempts=5): try: url = "urs.earthdata.nasa.gov" self.uid, _, self.pswd = netrc.netrc(self.netrc).authenticators(url) - session = self._start_session() + self._start_session() except: # if not using an environmental variable for password @@ -137,7 +137,7 @@ def login(self, attempts=5): self.pswd = getpass.getpass("Earthdata Login password: ") for i in range(attempts): try: - session = self._start_session() + self._start_session() break except KeyError: pass diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index 3fed2ef4f..5f4e455c6 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -259,7 +259,7 @@ def _default_varlists(product): else: print( - "THE REQUESTED PRODUCT DOES NOT YET HAVE A DEFAULT LIST SET UP. ONLY DELTA_TIME, LATITUTDE, AND LONGITUDE WILL BE RETURNED" + "THE REQUESTED PRODUCT DOES NOT YET HAVE A DEFAULT LIST SET UP. ONLY DELTA_TIME, LATITUDE, AND LONGITUDE WILL BE RETURNED" ) return common_list diff --git a/icepyx/core/query.py b/icepyx/core/query.py index 244e75978..db8219f8e 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -1017,7 +1017,7 @@ def download_granules( by default when subset=True, but additional subsetting options are available. Spatial subsetting returns all data that are within the area of interest (but not complete granules. This eliminates false-positive granules returned by the metadata-level search) - restart: boolean, default false + restart : boolean, default false If previous download was terminated unexpectedly. Run again with restart set to True to continue. **kwargs : key-value pairs Additional parameters to be passed to the subsetter. diff --git a/icepyx/core/read.py b/icepyx/core/read.py index e1624c2d6..d222c634c 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -311,9 +311,9 @@ def _check_source_for_pattern(source, filename_pattern): return False, None @staticmethod - def _add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): + def _add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): """ - Add the new variable group to the dataset template. + Add the new variables in the group to the dataset template. Parameters ---------- @@ -336,11 +336,9 @@ def _add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): Xarray Dataset with variables from the ds variable group added. """ - wanted_vars = list(wanted_dict.keys()) - if grp_path in ["orbit_info", "ancillary_data"]: grp_spec_vars = [ - wanted_vars[i] + wanted_groups_tiered[-1][i] for i, x in enumerate(wanted_groups_tiered[0]) if x == grp_path ] @@ -363,13 +361,21 @@ def _add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): pass try: - # DevNote: these lines may cause a NumPy Warning, as explained here: https://numpy.org/doc/stable/release/1.11.0-notes.html? - # The below line will silence this warning... - # warnings.filterwarnings( - # "default", category=DeprecationWarning, module=np.astype() - # ) - is2ds["data_start_utc"] = is2ds.data_start_utc.astype(np.datetime64) - is2ds["data_end_utc"] = is2ds.data_end_utc.astype(np.datetime64) + if ( + hasattr(is2ds, "data_start_utc") + and is2ds["data_start_utc"].data[0].astype(str).endswith("Z") + ): + # manually remove 'Z' from datetime to allow conversion to np.datetime64 object (support for timezones is deprecated and causes a seg fault) + is2ds["data_start_utc"] = np.datetime64( + is2ds.data_start_utc.data[0].astype(str)[:-1] + ) + is2ds["data_end_utc"] = np.datetime64( + is2ds.data_end_utc.data[0].astype(str)[:-1] + ) + else: + is2ds["data_start_utc"] = is2ds.data_start_utc.astype(np.datetime64) + is2ds["data_end_utc"] = is2ds.data_end_utc.astype(np.datetime64) + except AttributeError: pass @@ -381,9 +387,10 @@ def _add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): # add a test for the new function (called here)! grp_spec_vars = [ - k for k, v in wanted_dict.items() if any(grp_path in x for x in v) + k + for k, v in wanted_dict.items() + if any(f"{grp_path}/{k}" in x for x in v) ] - # print(grp_spec_vars) ds = ( ds.reset_coords(drop=False) @@ -392,17 +399,57 @@ def _add_var_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): .assign(gt=(("gran_idx", "spot"), [[gt_str]])) ) - # print(ds) grp_spec_vars.append("gt") is2ds = is2ds.merge( ds[grp_spec_vars], join="outer", combine_attrs="no_conflicts" ) - # print(is2ds) # re-cast some dtypes to make array smaller is2ds["gt"] = is2ds.gt.astype(str) is2ds["spot"] = is2ds.spot.astype(np.uint8) + return is2ds, ds[grp_spec_vars] + + @staticmethod + def _combine_nested_vars(is2ds, ds, grp_path, wanted_dict): + """ + Add the deeply nested variables to a dataset with appropriate coordinate information. + + Parameters + ---------- + is2ds : Xarray dataset + Dataset to add deeply nested variables to. + ds : Xarray dataset + Dataset containing proper dimensions for the variables being added + grp_path : str + hdf5 group path read into ds + wanted_dict : dict + Dictionary with variable names as keys and a list of group + variable paths containing those variables as values. + + Returns + ------- + Xarray Dataset with variables from the ds variable group added. + """ + + grp_spec_vars = [ + k for k, v in wanted_dict.items() if any(f"{grp_path}/{k}" in x for x in v) + ] + + # # Use this to handle issues specific to group paths that are more nested + # tiers = len(wanted_groups_tiered) + # if tiers > 3 and grp_path.count("/") == tiers - 2: + # # Handle attribute conflicts that arose from data descriptions during merging + # for var in grp_spec_vars: + # ds[var].attrs = ds.attrs + # for k in ds[var].attrs.keys(): + # ds.attrs.pop(k) + # # warnings.warn( + # # "Due to the number of layers of variable group paths, some attributes have been dropped from your DataSet during merging", + # # UserWarning, + # # ) + + is2ds = is2ds.assign(ds[grp_spec_vars]) + return is2ds def load(self): @@ -477,7 +524,7 @@ def _build_dataset_template(self, file): ) return is2ds - def _read_single_var(self, file, grp_path): + def _read_single_grp(self, file, grp_path): """ For a given file and variable group path, construct an Intake catalog and use it to read in the data. @@ -511,12 +558,10 @@ def _read_single_var(self, file, grp_path): grp_paths=grp_path, extra_engine_kwargs={"phony_dims": "access"}, ) - ds = grpcat[self._source_type].read() return ds - # NOTE: for non-gridded datasets only def _build_single_file_dataset(self, file, groups_list): """ Create a single xarray dataset with all of the wanted variables/groups from the wanted var list for a single data file/url. @@ -536,7 +581,7 @@ def _build_single_file_dataset(self, file, groups_list): Xarray Dataset """ - file_product = self._read_single_var(file, "/").attrs["identifier_product_type"] + file_product = self._read_single_grp(file, "/").attrs["identifier_product_type"] assert ( file_product == self._prod ), "Your product specification does not match the product specification within your files." @@ -569,13 +614,30 @@ def _build_single_file_dataset(self, file, groups_list): wanted_groups_set = set(wanted_groups) # orbit_info is used automatically as the first group path so the info is available for the rest of the groups wanted_groups_set.remove("orbit_info") + # Note: the sorting is critical for datasets with highly nested groups + wanted_groups_list = ["orbit_info"] + sorted(wanted_groups_set) # returns the wanted groups as a list of lists with group path string elements separated - _, wanted_groups_tiered = Variables.parse_var_list(groups_list, tiered=True) + _, wanted_groups_tiered = Variables.parse_var_list( + groups_list, tiered=True, tiered_vars=True + ) - for grp_path in ["orbit_info"] + list(wanted_groups_set): - ds = self._read_single_var(file, grp_path) - is2ds = Read._add_var_to_ds( + while wanted_groups_list: + grp_path = wanted_groups_list[0] + wanted_groups_list = wanted_groups_list[1:] + ds = self._read_single_grp(file, grp_path) + is2ds, ds = Read._add_vars_to_ds( is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict ) + # if there are any deeper nested variables, get those so they have actual coordinates and add them + if any(grp_path in grp_path2 for grp_path2 in wanted_groups_list): + for grp_path2 in wanted_groups_list: + if grp_path in grp_path2: + sub_ds = self._read_single_grp(file, grp_path2) + ds = Read._combine_nested_vars( + ds, sub_ds, grp_path2, wanted_dict + ) + wanted_groups_list.remove(grp_path2) + is2ds = is2ds.merge(ds, join="outer", combine_attrs="no_conflicts") + return is2ds diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index ef71dc737..ae12d4d3c 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -135,7 +135,7 @@ def visitor_func(name, node): return self._avail @staticmethod - def parse_var_list(varlist, tiered=True): + def parse_var_list(varlist, tiered=True, tiered_vars=False): """ Parse a list of path strings into tiered lists and names of variables @@ -149,6 +149,11 @@ def parse_var_list(varlist, tiered=True): (e.g. [['orbit_info', 'ancillary_data', 'gt1l'],['none','none','land_ice_segments']]) or a single list of path strings (e.g. ['orbit_info','ancillary_data','gt1l/land_ice_segments']) + tiered_vars : boolean, default False + Whether or not to append a list of the variable names to the nested list of component strings + (e.g. [['orbit_info', 'ancillary_data', 'gt1l'],['none','none','land_ice_segments'], + ['sc_orient','atlas_sdp_gps_epoch','h_li']])) + Examples -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28'], version='1') # doctest: +SKIP @@ -215,7 +220,10 @@ def parse_var_list(varlist, tiered=True): else: num = np.max([v.count("/") for v in varlist]) # print('max needed: ' + str(num)) - paths = [[] for i in range(num)] + if tiered_vars == True: + paths = [[] for i in range(num + 1)] + else: + paths = [[] for i in range(num)] # print(self._cust_options['variables']) for vn in varlist: @@ -237,6 +245,8 @@ def parse_var_list(varlist, tiered=True): for i in range(j, num): paths[i].append("none") i = i + 1 + if tiered_vars == True: + paths[num].append(vkey) return vgrp, paths diff --git a/icepyx/tests/conftest.py b/icepyx/tests/conftest.py index c0dfda45a..8ec8f6cfb 100644 --- a/icepyx/tests/conftest.py +++ b/icepyx/tests/conftest.py @@ -5,20 +5,27 @@ # PURPOSE: mock environmental variables @pytest.fixture(scope="session", autouse=True) def mock_settings_env_vars(): - with mock.patch.dict("os.environ", { - "EARTHDATA_USERNAME": "icepyx_devteam", - "EARTHDATA_PASSWORD": os.environ.get("NSIDC_LOGIN"), - "EARTHDATA_EMAIL": "icepyx.dev@gmail.com"}): + with mock.patch.dict( + "os.environ", + { + "EARTHDATA_USERNAME": "icepyx_devteam", + "EARTHDATA_PASSWORD": "fake_earthdata_password", + "EARTHDATA_EMAIL": "icepyx.dev@gmail.com", + }, + ): yield + @pytest.fixture(scope="session") def username(): - return os.environ.get('EARTHDATA_USERNAME') + return os.environ.get("EARTHDATA_USERNAME") + @pytest.fixture(scope="session") def password(): - return os.environ.get('EARTHDATA_PASSWORD') + return os.environ.get("EARTHDATA_PASSWORD") + @pytest.fixture(scope="session") def email(): - return os.environ.get('EARTHDATA_EMAIL') + return os.environ.get("EARTHDATA_EMAIL") diff --git a/icepyx/tests/test_behind_NSIDC_API_login.py b/icepyx/tests/test_behind_NSIDC_API_login.py index 1f7469383..a277fcd35 100644 --- a/icepyx/tests/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/test_behind_NSIDC_API_login.py @@ -10,22 +10,27 @@ # check that downloaded data is subset? or is this an NSIDC level test so long as we verify the right info is submitted? -@pytest.fixture -def reg(scope="module"): - return ipx.Query( +@pytest.fixture(scope="module") +def reg(): + live_reg = ipx.Query( "ATL06", [-55, 68, -48, 71], ["2019-02-22", "2019-02-28"], version="004" ) + yield live_reg + del live_reg -@pytest.fixture -def session(reg, scope="module"): +@pytest.fixture(scope="module") +def session(reg): capability_url = f"https://n5eil02u.ecs.nsidc.org/egi/capabilities/{reg.product}.{reg._version}.xml" - return Earthdata( + ed_obj = Earthdata( "icepyx_devteam", "icepyx.dev@gmail.com", capability_url=capability_url, pswd=os.getenv("NSIDC_LOGIN"), - )._start_session() + ) + ed_obj._start_session() + yield ed_obj.session + ed_obj.session.close() ########## is2ref module ########## @@ -35,7 +40,8 @@ def session(reg, scope="module"): def test_get_custom_options_output(session): obs = is2ref._get_custom_options(session, "ATL06", "004") - with open("./ATL06v04_options.json", "r") as exp: + with open("./icepyx/tests/ATL06v04_options.json") as exp_json: + exp = json.load(exp_json) assert all(keys in obs.keys() for keys in exp.keys()) assert all(obs[key] == exp[key] for key in exp.keys()) @@ -44,8 +50,9 @@ def test_get_custom_options_output(session): # NOTE: best this test can do at the moment is a successful download with no errors... def test_download_granules_with_subsetting(reg, session): path = "./downloads_subset" - reg.order_granules(session) - reg.download_granules(session, path) + reg._session = session + reg.order_granules() + reg.download_granules(path) # def test_download_granules_without_subsetting(reg_a, session):