From c0ed05f841875e10d8314b8eca48f07b12608c77 Mon Sep 17 00:00:00 2001 From: Andrew Scherer Date: Tue, 22 Apr 2025 12:02:00 -0700 Subject: [PATCH 1/2] Adds support for multidimensional array inputs to the algorithm --- pycoare/coare_35.py | 58 +++++++++++++++++++++---------------------- pycoare/coare_36.py | 60 ++++++++++++++++++++++----------------------- pycoare/util.py | 22 +++++++++-------- 3 files changed, 71 insertions(+), 69 deletions(-) diff --git a/pycoare/coare_35.py b/pycoare/coare_35.py index 7e90765..8966fc8 100644 --- a/pycoare/coare_35.py +++ b/pycoare/coare_35.py @@ -197,34 +197,34 @@ def __post_init__(self): def _sanitize(self): self.u = np.asarray(self.u, dtype=np.float64) - self.N = self.u.size - self.t = _check_size(self.t, self.N, "t") - self.rh = _check_size(self.rh, self.N, "rh") - self.zu = _check_size(self.zu, self.N, "zu") - self.zt = _check_size(self.zq, self.N, "zq") - self.zq = _check_size(self.zt, self.N, "zt") - self.zrf = _check_size(self.zrf, self.N, "zrf") - self.us = _check_size(self.us, self.N, "us") - self.ts = _check_size(self.ts, self.N, "ts") - self.p = _check_size(self.p, self.N, "p") - self.lat = _check_size(self.lat, self.N, "Lat") - self.zi = _check_size(self.zi, self.N, "zi") - self.rs = _check_size(self.rs, self.N, "rs") - self.rl = _check_size(self.rl, self.N, "rl") - self.rain = _check_size(self.rain, self.N, "rain") + self.shape = self.u.shape + self.t = _check_size(self.t, self.shape, "t") + self.rh = _check_size(self.rh, self.shape, "rh") + self.zu = _check_size(self.zu, self.shape, "zu") + self.zt = _check_size(self.zq, self.shape, "zq") + self.zq = _check_size(self.zt, self.shape, "zt") + self.zrf = _check_size(self.zrf, self.shape, "zrf") + self.us = _check_size(self.us, self.shape, "us") + self.ts = _check_size(self.ts, self.shape, "ts") + self.p = _check_size(self.p, self.shape, "p") + self.lat = _check_size(self.lat, self.shape, "Lat") + self.zi = _check_size(self.zi, self.shape, "zi") + self.rs = _check_size(self.rs, self.shape, "rs") + self.rl = _check_size(self.rl, self.shape, "rl") + self.rain = _check_size(self.rain, self.shape, "rain") # set waveage and seastate flags if self.cp is not None: self.waveage_flag = ~np.isnan(self.cp) - self.cp = _check_size(self.cp, self.N, "cp") + self.cp = _check_size(self.cp, self.shape, "cp") else: self.waveage_flag = False - self.cp = np.nan * np.ones(self.N) + self.cp = np.nan * np.ones(self.shape) if self.sigH is not None: self.seastate_flag = ~np.isnan(self.sigH) & self.waveage_flag - self.sigH = _check_size(self.sigH, self.N, "sigH") + self.sigH = _check_size(self.sigH, self.shape, "sigH") else: self.seastate_flag = False - self.sigH = np.nan * np.ones(self.N) + self.sigH = np.nan * np.ones(self.shape) # check jcool if self.jcool != 0: self.jcool = 1 # all input other than 0 defaults to jcool=1 @@ -822,7 +822,7 @@ def _bulk_loop(self): usr, tsr, qsr = self._get_star( ut, dt, dq, dter, zo10, zot10, np.nan, obukL10, setup=True ) - tkt = 0.001 * np.ones(_bulk_loop_inputs.N) + tkt = 0.001 * np.ones(_bulk_loop_inputs.shape) charnC, charnW, charnS = self._get_charn(u10, usr, setup=True) for i in range(_bulk_loop_inputs.nits): @@ -852,8 +852,8 @@ def _bulk_loop(self): ug = self._get_ug(ta, usr, tvsr) ut = np.sqrt(du**2 + ug**2) # probably a better way to do this, but this avoids a divide by zero runtime warning - gf = np.full(_bulk_loop_inputs.N, np.inf) - k = np.flatnonzero(du != 0) + gf = np.full(_bulk_loop_inputs.shape, np.inf) + k = du != 0 gf[k] = ut[k] / du[k] tkt, dter, dqer = self._get_cool_skin(usr, tsr, qsr, tkt, rnl) @@ -920,8 +920,8 @@ def _get_dudtdq(self): def _get_ug(self, ta, usr, tvsr): _bulk_loop_inputs = self._bulk_loop_inputs Bf = -_bulk_loop_inputs.grav / ta * usr * tvsr - ug = 0.2 * np.ones(_bulk_loop_inputs.N) - k = np.flatnonzero(Bf > 0) + ug = 0.2 * np.ones(_bulk_loop_inputs.shape) + k = Bf > 0 if _bulk_loop_inputs.zrf.size == 1: ug[k] = self.BETA * (Bf[k] * _bulk_loop_inputs.zi) ** (1 / 3) else: @@ -946,9 +946,9 @@ def _get_mo_stability_setup(self, ta, ut, zo, dt, dq, dter): / ut**2 ) zetu = cc * ribu * (1 + 27 / 9 * ribu / cc) - k50 = np.flatnonzero(zetu > 50) # stable with thin M-O length relative to zu + k50 = zetu > 50 # stable with thin M-O length relative to zu - k = np.flatnonzero(ribu < 0) + k = ribu < 0 if ribcu.size == 1: zetu[k] = cc[k] * ribu[k] / (1 + ribu[k] / ribcu) else: @@ -959,7 +959,7 @@ def _get_charn(self, u, usr, setup=False): _bulk_loop_inputs = self._bulk_loop_inputs # The following gives the new formulation for the Charnock variable charnC = self.A1 * u + self.A2 - k = np.flatnonzero(u > self.UMAX) + k = u > self.UMAX charnC[k] = self.A1 * self.UMAX + self.A2 charnW = self.A * (usr / _bulk_loop_inputs.cp) ** self.B if setup: @@ -1074,12 +1074,12 @@ def _get_cool_skin(self, usr, tsr, qsr, tkt, rnl): _bulk_loop_inputs.al * qcol + self.BE * hlb * self.CPW / _bulk_loop_inputs.lhvap ) - xlamx = 6.0 * np.ones(_bulk_loop_inputs.N) + xlamx = 6.0 * np.ones(_bulk_loop_inputs.shape) tkt = np.minimum( 0.01, xlamx * self.VISW / (np.sqrt(_bulk_loop_inputs.rhoa / self.RHOW) * usr), ) - k = np.flatnonzero(alq > 0) + k = alq > 0 xlamx[k] = ( 6 / (1 + (_bulk_loop_inputs.bigc[k] * alq[k] / usr[k] ** 4) ** 0.75) ** 0.333 diff --git a/pycoare/coare_36.py b/pycoare/coare_36.py index a735181..bb88857 100644 --- a/pycoare/coare_36.py +++ b/pycoare/coare_36.py @@ -186,35 +186,35 @@ def __post_init__(self): def _sanitize(self): self.u = np.asarray(self.u, dtype=np.float64) - self.N = self.u.size - self.t = _check_size(self.t, self.N, "t") - self.rh = _check_size(self.rh, self.N, "rh") - self.zu = _check_size(self.zu, self.N, "zu") - self.zt = _check_size(self.zq, self.N, "zq") - self.zq = _check_size(self.zt, self.N, "zt") - self.zrf = _check_size(self.zrf, self.N, "zrf") - self.us = _check_size(self.us, self.N, "us") - self.ts = _check_size(self.ts, self.N, "ts") - self.ss = _check_size(self.ss, self.N, "ss") - self.p = _check_size(self.p, self.N, "p") - self.lat = _check_size(self.lat, self.N, "lat") - self.zi = _check_size(self.zi, self.N, "zi") - self.rs = _check_size(self.rs, self.N, "rs") - self.rl = _check_size(self.rl, self.N, "rl") - self.rain = _check_size(self.rain, self.N, "rain") + self.shape = self.u.shape + self.t = _check_size(self.t, self.shape, "t") + self.rh = _check_size(self.rh, self.shape, "rh") + self.zu = _check_size(self.zu, self.shape, "zu") + self.zt = _check_size(self.zq, self.shape, "zq") + self.zq = _check_size(self.zt, self.shape, "zt") + self.zrf = _check_size(self.zrf, self.shape, "zrf") + self.us = _check_size(self.us, self.shape, "us") + self.ts = _check_size(self.ts, self.shape, "ts") + self.ss = _check_size(self.ss, self.shape, "ss") + self.p = _check_size(self.p, self.shape, "p") + self.lat = _check_size(self.lat, self.shape, "lat") + self.zi = _check_size(self.zi, self.shape, "zi") + self.rs = _check_size(self.rs, self.shape, "rs") + self.rl = _check_size(self.rl, self.shape, "rl") + self.rain = _check_size(self.rain, self.shape, "rain") # set waveage and seastate flags if self.cp is not None: self.waveage_flag = ~np.isnan(self.cp) - self.cp = _check_size(self.cp, self.N, "cp") + self.cp = _check_size(self.cp, self.shape, "cp") else: self.waveage_flag = False - self.cp = np.nan * np.ones(self.N) + self.cp = np.nan * np.ones(self.shape) if self.sigH is not None: self.seastate_flag = ~np.isnan(self.sigH) & self.waveage_flag - self.sigH = _check_size(self.sigH, self.N, "sigH") + self.sigH = _check_size(self.sigH, self.shape, "sigH") else: self.seastate_flag = False - self.sigH = np.nan * np.ones(self.N) + self.sigH = np.nan * np.ones(self.shape) # check jcool if self.jcool != 0: self.jcool = 1 # all input other than 0 defaults to jcool=1 @@ -344,7 +344,7 @@ def _bulk_loop(self): usr, tsr, qsr = self._get_star( ut, dt, dq, dter, zo10, zot10, np.nan, obukL10, setup=True ) - tkt = 0.001 * np.ones(_bulk_loop_inputs.N) + tkt = 0.001 * np.ones(_bulk_loop_inputs.shape) charnC, charnS = self._get_charn(u10, usr, setup=True) for i in range(_bulk_loop_inputs.nits): @@ -375,8 +375,8 @@ def _bulk_loop(self): ug = self._get_ug(ta, usr, tvsr) ut = np.sqrt(du**2 + ug**2) # probably a better way to do this, but this avoids a divide by zero runtime warning - gf = np.full(_bulk_loop_inputs.N, np.inf) - k = np.flatnonzero(du != 0) + gf = np.full(_bulk_loop_inputs.shape, np.inf) + k = du != 0 gf[k] = ut[k] / du[k] tkt, dter, dqer = self._get_cool_skin(usr, tsr, qsr, tkt, rnl) @@ -449,8 +449,8 @@ def _get_dudtdq(self): def _get_ug(self, ta, usr, tvsr): _bulk_loop_inputs = self._bulk_loop_inputs Bf = -_bulk_loop_inputs.grav / ta * usr * tvsr - ug = 0.2 * np.ones(_bulk_loop_inputs.N) - k = np.flatnonzero(Bf > 0) + ug = 0.2 * np.ones(_bulk_loop_inputs.shape) + k = Bf > 0 if _bulk_loop_inputs.zrf.size == 1: ug[k] = self.BETA * (Bf[k] * _bulk_loop_inputs.zi) ** (1 / 3) else: @@ -475,9 +475,9 @@ def _get_mo_stability_setup(self, ta, ut, zo, dt, dq, dter): / ut**2 ) zetu = cc * ribu * (1 + 27 / 9 * ribu / cc) - k50 = np.flatnonzero(zetu > 50) # stable with thin M-O length relative to zu + k50 = zetu > 50 # stable with thin M-O length relative to zu - k = np.flatnonzero(ribu < 0) + k = ribu < 0 if ribcu.size == 1: zetu[k] = cc[k] * ribu[k] / (1 + ribu[k] / ribcu) else: @@ -488,7 +488,7 @@ def _get_charn(self, u, usr, setup=False): _bulk_loop_inputs = self._bulk_loop_inputs # The following gives the new formulation for the Charnock variable charnC = self.A1 * u + self.A2 - charnC[np.flatnonzero(u > self.UMAX)] = self.A1 * self.UMAX + self.A2 + charnC[u > self.UMAX] = self.A1 * self.UMAX + self.A2 # if wave age is given but not wave height, use parameterized wave height based on wind speed mask = np.isnan(_bulk_loop_inputs.sigH) & _bulk_loop_inputs.waveage_flag _bulk_loop_inputs.sigH[mask] = np.maximum( @@ -608,12 +608,12 @@ def _get_cool_skin(self, usr, tsr, qsr, tkt, rnl): _bulk_loop_inputs.al * qcol + self.BE * hlb * self.CPW / _bulk_loop_inputs.lhvap ) - xlamx = 6.0 * np.ones(_bulk_loop_inputs.N) + xlamx = 6.0 * np.ones(_bulk_loop_inputs.shape) tkt = np.minimum( 0.01, xlamx * self.VISW / (np.sqrt(_bulk_loop_inputs.rhoa / self.RHOW) * usr), ) - k = np.flatnonzero(alq > 0) + k = alq > 0 xlamx[k] = ( 6 / (1 + (_bulk_loop_inputs.bigc[k] * alq[k] / usr[k] ** 4) ** 0.75) ** 0.333 diff --git a/pycoare/util.py b/pycoare/util.py index 3ce31d4..702957e 100644 --- a/pycoare/util.py +++ b/pycoare/util.py @@ -108,7 +108,7 @@ def psit_26(z_L: ArrayLike) -> NDArray[np.float64]: :return: temperature structure function :rtype: NDArray[np.float64] """ - zet = np.copy(np.asarray(z_L, dtype=float)) # conversion to ndarray float + zet = np.asarray(z_L, dtype=float) # compute psi_t for stable conditions by Beljaars & Holtslag 1991 a = 1 b = 0.6667 @@ -117,7 +117,7 @@ def psit_26(z_L: ArrayLike) -> NDArray[np.float64]: dzet = d * zet dzet[dzet > 50] = 50.0 psi = np.nan * np.empty(zet.shape, dtype=float) - k = np.flatnonzero(zet >= 0) + k = zet >= 0 psi[k] = -( (1 + 2 / 3 * a * zet[k]) ** (3 / 2) + b * (zet[k] - c / d) * np.exp(-dzet[k]) @@ -125,7 +125,7 @@ def psit_26(z_L: ArrayLike) -> NDArray[np.float64]: - 1 ) # compute convective psi_t for unstable conditions by Grachev et. al., 2000 - k = np.flatnonzero(zet < 0) + k = zet < 0 x = (1 - 15 * zet[k]) ** (1 / 2) psik = 2 * np.log((1 + x) / 2.0) # kansas psi x = (1 - 34.15 * zet[k]) ** (1 / 3) @@ -148,7 +148,7 @@ def psiu_26(z_L: ArrayLike) -> NDArray[np.float64]: :return: velocity structure function :rtype: NDArray[np.float64] """ - zet = np.copy(np.asarray(z_L, dtype=float)) # conversion to ndarray float + zet = np.asarray(z_L, dtype=float) # compute psi_u for stable conditions by Beljaars & Holtslag 1991 a = 0.7 b = 3.0 / 4.0 @@ -157,10 +157,10 @@ def psiu_26(z_L: ArrayLike) -> NDArray[np.float64]: dzet = d * zet dzet[dzet > 50] = 50.0 psi = np.nan * np.empty(zet.shape, dtype=float) - k = np.flatnonzero(zet >= 0) + k = zet >= 0 psi[k] = -(a * zet[k] + b * (zet[k] - c / d) * np.exp(-dzet[k]) + b * c / d) # compute convective psi for unstable conditions by Grachev et. al., 2000 - k = np.flatnonzero(zet < 0) # only compute where zet < 0 + k = zet < 0 # only compute where zet < 0 x = (1 - 15 * zet[k]) ** (1 / 4) psik = ( 2.0 * np.log((1.0 + x) / 2.0) @@ -188,7 +188,7 @@ def psiu_40(z_L: ArrayLike) -> NDArray[np.float64]: :return: velocity structure function :rtype: NDArray[np.float64] """ - zet = np.copy(np.asarray(z_L, dtype=float)) + zet = np.asarray(z_L, dtype=float) # compute psi_u for stable conditions by Beljaars & Holtslag 1991 a = 1.0 b = 3.0 / 4.0 @@ -197,7 +197,7 @@ def psiu_40(z_L: ArrayLike) -> NDArray[np.float64]: dzet = d * zet dzet[dzet > 50] = 50.0 psi = np.nan * np.empty(zet.shape, dtype=float) - k = np.flatnonzero(zet >= 0) + k = zet >= 0 psi[k] = -(a * zet[k] + b * (zet[k] - c / d) * np.exp(-dzet[k]) + b * c / d) # compute convective psi for unstable conditions by Grachev et. al., 2000 k = np.flatnonzero(zet < 0) @@ -224,8 +224,10 @@ def _check_size( arr: ArrayLike, N: int, name: str = "Input", warn=False ) -> NDArray[np.float64]: arr = np.asarray(arr, dtype=float) - if arr.size != N and arr.size != 1: - raise ValueError(f"pyCOARE: {name} array of different length than u") + if arr.shape != N and arr.size != 1: + raise ValueError( + f"pyCOARE: {name} array of shape {arr.shape} different shape than u array of shape {N}" + ) elif arr.size == 1: if warn: print(f"pyCOARE: {name} array of length 1, broadcasting to length {N}") From 0bada7e129c7144eaeb4375e0d62950e3cbd2bfe Mon Sep 17 00:00:00 2001 From: Andrew Scherer Date: Tue, 22 Apr 2025 12:02:52 -0700 Subject: [PATCH 2/2] Bump version number, add pytest as dev dependency, and drop Python 3.8 support (which should have been done a few PRs ago) --- pyproject.toml | 7 +- uv.lock | 267 ++++++++++++------------------------------------- 2 files changed, 68 insertions(+), 206 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 34891a5..21a8bc3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,10 +6,10 @@ build-backend = "setuptools.build_meta" name = "pycoare" authors = [{ name = 'Andrew Scherer', email = 'scherand@oregonstate.edu' }] maintainers = [{ name = 'Andrew Scherer', email = 'scherand@oregonstate.edu' }] -version = "0.2.3" +version = "0.3.0" description = 'A Python implementation of the COARE bulk air-sea flux algorithm.' readme = { file = 'README.md', content-type = 'text/markdown' } -requires-python = ">=3.8" +requires-python = ">=3.9" keywords = ['oceanography', 'air-sea', 'bulk flux'] license = { text = "MIT License" } classifiers = [ @@ -24,3 +24,6 @@ dependencies = ['numpy'] [project.urls] Source = 'https://github.com/pyCOARE/coare' + +[dependency-groups] +dev = ["pytest>=8.3.5"] diff --git a/uv.lock b/uv.lock index 835bd82..e8d8f4c 100644 --- a/uv.lock +++ b/uv.lock @@ -6,15 +6,6 @@ resolution-markers = [ "python_full_version < '3.10'", ] -[[package]] -name = "cfgv" -version = "3.4.0" -source = { registry = 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